LAMMPS (30 Aug 2013) units metal variable E equal 20.0 variable nx equal 16 # allow charges atom_style full dielectric 1. dimension 3 boundary p p p lattice fcc 4.08 origin 0.25 0.25 0.25 Lattice spacing in x,y,z = 4.08 4.08 4.08 region BOX block -8 8 0 3 0 3 create_box 3 BOX Created orthogonal box = (-32.64 0 0) to (32.64 12.24 12.24) 4 by 1 by 1 MPI processor grid create_atoms 1 region BOX Created 576 atoms pair_style lj/cut 10. #pair_style lj/cut/coul/long 10. #kspace_style pppm 1.e-4 #kspace_style ewald 1.e-4 pair_coeff * * 0.2381 3.405 mass * 39.948 group real region BOX 576 atoms in group real region LEFT block -5 -2 INF INF INF INF region RIGHT block 2 5 INF INF INF INF set region LEFT type 2 Setting atom values ... 108 settings made for type set region RIGHT type 3 Setting atom values ... 108 settings made for type set region LEFT charge -1. Setting atom values ... 108 settings made for charge set region RIGHT charge 1. Setting atom values ... 108 settings made for charge group NION region LEFT 108 atoms in group NION group PION region RIGHT 108 atoms in group PION neighbor 2. bin ########################################################################### #fix EFIELD all efield $E 0.0 0.0 ########################################################################### fix ATC real atc species_electrostatic Ar_species.mat ATC: constructing electrostatic species coupling with parameter file Ar_species.mat ATC: version 2.0 ATC: peratom PE compute created with ID: 3 ATC: WARNING: material units real do not match lammps ATC: 1 materials defined from Ar_species.mat ATC: creating fem_efield extrinsic model ATC: WARNING: material units real do not match lammps ATC: 1 materials defined from Ar_species.mat fix_modify ATC add_species N group NION fix_modify ATC add_species P group PION fix_modify ATC include atomic_charge fix_modify ATC internal_quadrature off fix_modify ATC extrinsic short_range off fix_modify ATC mesh create ${nx} 1 1 BOX p p p fix_modify ATC mesh create 16 1 1 BOX p p p ATC: created uniform mesh with 68 nodes, 16 unique nodes, and 16 elements fix_modify ATC atom_element_map eulerian 1 fix_modify ATC atom_weight multiscale fix_modify ATC initial mass_density all 0. #fix_modify ATC initial charge_density all 0. fix_modify ATC initial electric_potential all 0. fix_modify ATC mesh create_nodeset left_end -8.01 -7.99 -.1 .1 -.1 .1 ATC: created nodeset left_end with 1 nodes fix_modify ATC fix electric_potential left_end 0. #fix_modify ATC mesh create_nodeset right_end 7.99 8.01 -.1 .1 -.1 .1 #fix_modify ATC fix electric_potential right_end 0. # quick test for charged surfaces #fix_modify ATC mesh create_faceset left_end box -8 10 -10 10 -10 10 outward #fix_modify ATC extrinsic fix_charge left_end 0. fix_modify ATC add_species NION type 2 fix_modify ATC add_species PION type 3 ########################################################################### variable n equal count(real) print "number of atoms: $n" number of atoms: 576 timestep 0.0005 thermo 100 compute Fn NION reduce sum fx compute Fp PION reduce sum fx thermo_style custom step etotal temp press pe c_Fn c_Fp # initial thermo line should be: #0 13699.992 0 12453927 13699.992 880.49388 -880.49388 fix_modify ATC output opp_forceFE 100 text binary ATC: Warning : text output can create _LARGE_ files ATC: output custom names: NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationNION NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationPION NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationN NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationP species_concentration : species_concentrationNION species_concentration : species_concentrationPION species_concentration : species_concentrationN species_concentration : species_concentrationP run 1000 Setting up run ... ATC: WARNING: material: [ar] cannot find mass_density ATC: WARNING: physics model: [species], material: [ar] does not provide all interfaces for physics and will be treated as null 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: material: [ar] cannot find mass_density ATC: WARNING: physics model: [species electrostatic], material: [ar] does not provide all interfaces for physics and will be treated as null Memory usage per processor = 50.4595 Mbytes Step TotEng Temp Press PotEng Fn Fp 0 13699.992 0 12453927 13699.992 880.49388 -880.49388 100 18516.206 19920.46 14980264 17035.627 -29.468216 29.468216 200 18590.499 18996.496 15042503 17178.592 74.632418 -74.632418 300 16986.906 22207.446 13773775 15336.347 213.36855 -213.36855 400 17031.316 20483.897 13881842 15508.858 -1030.06 1030.06 500 18393.547 13569.054 15141293 17385.033 -881.32991 881.32991 600 17629.245 22129.326 14228700 15984.492 297.77405 -297.77405 700 17374.698 17398.728 14252085 16081.545 -1458.7112 1458.7112 800 17805.47 15491.378 14643513 16654.08 2644.7457 -2644.7457 900 20614.308 23711.81 16239209 18851.938 218.5282 -218.5282 1000 22067.741 26242.181 17175599 20117.302 -752.00587 752.00587 Loop time of 3.62172 on 4 procs for 1000 steps with 576 atoms Pair time (%) = 1.48902 (41.1135) Bond time (%) = 0.000212669 (0.00587205) Neigh time (%) = 0.0337982 (0.933206) Comm time (%) = 0.176507 (4.87357) Outpt time (%) = 0.0090723 (0.250497) Other time (%) = 1.91312 (52.8234) Nlocal: 144 ave 144 max 144 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 3096 ave 3096 max 3096 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 30906 ave 31490 max 30319 min Histogram: 2 0 0 0 0 0 0 0 0 2 FullNghs: 61812 ave 62964 max 60660 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 247248 Ave neighs/atom = 429.25 Ave special neighs/atom = 0 Neighbor list builds = 7 Dangerous builds = 0