LAMMPS (30 Aug 2013) units metal variable E equal 20.0 variable nx equal 32 # allow charges atom_style full dielectric 1. dimension 3 boundary f 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 0 16 0 3 0 3 create_box 1 BOX Created orthogonal box = (0 0 0) to (65.28 12.24 12.24) 4 by 1 by 1 MPI processor grid create_atoms 1 region BOX Created 576 atoms pair_style lj/cut 13. pair_coeff * * 0.2381 3.405 mass * 39.948 group real region BOX 576 atoms in group real set group real charge 1 Setting atom values ... 576 settings made for charge ########################################################################### #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 ion type 1 ### <<<<< #fix_modify ATC add_species REAL group real 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 f p p fix_modify ATC mesh create 32 1 1 BOX f p p ATC: created uniform mesh with 132 nodes, 33 unique nodes, and 32 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. ########################################################################### variable n equal count(real) print "number of atoms: $n" number of atoms: 576 timestep 0.0 thermo 1 compute Fx real reduce sum fx compute Fy real reduce sum fy thermo_style custom step etotal temp press pe c_Fx c_Fy fix_modify ATC output poissonFE 1 text binary ATC: Warning : text output can create _LARGE_ files ATC: output custom names: NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationion species_concentration : species_concentrationion # (1) all fixed fix_modify ATC fix electric_potential all linear 0 0 0 $E 0 0 0 0 fix_modify ATC fix electric_potential all linear 0 0 0 20 0 0 0 0 ATC: created function : 0 + 20(x-0)+0(y-0)+0(z-0) run 1 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 = 48.9866 Mbytes Step TotEng Temp Press PotEng Fx Fy 0 13388.811 0 12185513 13388.811 -11520 -5.4091662e-13 1 13388.811 0 12185513 13388.811 -11520 -5.4091662e-13 Loop time of 0.00854391 on 4 procs for 1 steps with 576 atoms Pair time (%) = 0.00297153 (34.7795) Bond time (%) = 7.7486e-07 (0.00906916) Neigh time (%) = 0 (0) Comm time (%) = 0.000446737 (5.22872) Outpt time (%) = 0.00115174 (13.4803) Other time (%) = 0.00397313 (46.5024) Nlocal: 144 ave 144 max 144 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 3556 ave 4256 max 2856 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 58212 ave 63792 max 52524 min Histogram: 2 0 0 0 0 0 0 0 0 2 FullNghs: 116424 ave 127584 max 105264 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 465696 Ave neighs/atom = 808.5 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 # (2) Dirichlet # NOTE with correct density solution is very close #fix_modify ATC fix charge_density all 0.0588951459091903 fix_modify ATC unfix electric_potential all fix_modify ATC mesh create_nodeset lbc 0.0 0.0 -INF INF -INF INF ATC: created nodeset lbc with 1 nodes fix_modify ATC mesh create_faceset lbc 0.0 INF -INF INF -INF INF ATC: created faceset lbc with 1 faces fix_modify ATC mesh create_faceset rbc -INF 16.0 -INF INF -INF INF ATC: created faceset rbc with 1 faces fix_modify ATC fix electric_potential lbc 100.0 run 1 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: 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 = 48.9866 Mbytes Step TotEng Temp Press PotEng Fx Fy 1 13388.811 0 12185513 13388.811 -200361.27 6.719863e-13 2 13388.811 0 12185513 13388.811 -200361.27 6.719863e-13 Loop time of 0.00797898 on 4 procs for 1 steps with 576 atoms Pair time (%) = 0.00296175 (37.1195) Bond time (%) = 2.38419e-07 (0.00298809) Neigh time (%) = 0 (0) Comm time (%) = 0.000458777 (5.74982) Outpt time (%) = 0.000847757 (10.6249) Other time (%) = 0.00371045 (46.5028) Nlocal: 144 ave 144 max 144 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 3556 ave 4256 max 2856 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 58212 ave 63792 max 52524 min Histogram: 2 0 0 0 0 0 0 0 0 2 FullNghs: 116424 ave 127584 max 105264 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 465696 Ave neighs/atom = 808.5 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 # (3) Neumann fix_modify ATC fix_flux electric_potential rbc 0.5 run 1 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: 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 = 48.9866 Mbytes Step TotEng Temp Press PotEng Fx Fy 2 13388.811 0 12185513 13388.811 -252475.24 1.1650611e-12 3 13388.811 0 12185513 13388.811 -252475.24 1.1650611e-12 Loop time of 0.00814193 on 4 procs for 1 steps with 576 atoms Pair time (%) = 0.0029577 (36.3268) Bond time (%) = 2.98023e-07 (0.00366035) Neigh time (%) = 0 (0) Comm time (%) = 0.000454485 (5.58203) Outpt time (%) = 0.000847459 (10.4086) Other time (%) = 0.00388199 (47.679) Nlocal: 144 ave 144 max 144 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 3556 ave 4256 max 2856 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 58212 ave 63792 max 52524 min Histogram: 2 0 0 0 0 0 0 0 0 2 FullNghs: 116424 ave 127584 max 105264 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 465696 Ave neighs/atom = 808.5 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 # (4) Robin eps_1 phi'_1 = eps_2/L_2 (phi_{L_2} - phi) fix_modify ATC unfix_flux electric_potential rbc fix_modify ATC fix_robin electric_potential rbc 0.5 -0.00001 ATC: created function : 0.5 + -1e-05*u run 1 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: 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 = 48.9866 Mbytes Step TotEng Temp Press PotEng Fx Fy 3 13388.811 0 12185513 13388.811 -225709.12 9.1181426e-13 4 13388.811 0 12185513 13388.811 -225709.12 9.1181426e-13 Loop time of 0.00825572 on 4 procs for 1 steps with 576 atoms Pair time (%) = 0.00296426 (35.9055) Bond time (%) = 7.15256e-07 (0.00866376) Neigh time (%) = 0 (0) Comm time (%) = 0.000457525 (5.54192) Outpt time (%) = 0.000843704 (10.2196) Other time (%) = 0.00398952 (48.3243) Nlocal: 144 ave 144 max 144 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 3556 ave 4256 max 2856 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 58212 ave 63792 max 52524 min Histogram: 2 0 0 0 0 0 0 0 0 2 FullNghs: 116424 ave 127584 max 105264 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 465696 Ave neighs/atom = 808.5 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 # (5) Robins on the left and Robins on the right fix_modify ATC unfix electric_potential lbc fix_modify ATC fix_robin electric_potential rbc 0.01 -0.0001 ATC: created function : 0.01 + -0.0001*u fix_modify ATC fix_robin electric_potential lbc 0.01 -0.0001 ATC: created function : 0.01 + -0.0001*u run 1 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: 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 = 48.9866 Mbytes Step TotEng Temp Press PotEng Fx Fy 4 13388.811 0 12185513 13388.811 4.3291948e-09 -1.4571568e-12 5 13388.811 0 12185513 13388.811 4.3364707e-09 -1.4571568e-12 Loop time of 0.00868404 on 4 procs for 1 steps with 576 atoms Pair time (%) = 0.00308079 (35.4764) Bond time (%) = 2.38419e-07 (0.00274548) Neigh time (%) = 0 (0) Comm time (%) = 0.000677586 (7.80265) Outpt time (%) = 0.000885546 (10.1974) Other time (%) = 0.00403988 (46.5208) Nlocal: 144 ave 144 max 144 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 3556 ave 4256 max 2856 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 58212 ave 63792 max 52524 min Histogram: 2 0 0 0 0 0 0 0 0 2 FullNghs: 116424 ave 127584 max 105264 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 465696 Ave neighs/atom = 808.5 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 #fix_modify ATC fix charge_density all 0.0 #run 1