1LAMMPS (30 Aug 2013) 2units metal 3variable E equal 20.0 4variable nx equal 32 5# allow charges 6atom_style full 7dielectric 1. 8dimension 3 9boundary f p p 10lattice fcc 4.08 origin 0.25 0.25 0.25 11Lattice spacing in x,y,z = 4.08 4.08 4.08 12region BOX block 0 16 0 3 0 3 13create_box 1 BOX 14Created orthogonal box = (0 0 0) to (65.28 12.24 12.24) 15 4 by 1 by 1 MPI processor grid 16create_atoms 1 region BOX 17Created 576 atoms 18pair_style lj/cut 13. 19pair_coeff * * 0.2381 3.405 20mass * 39.948 21group real region BOX 22576 atoms in group real 23set group real charge 1 24Setting atom values ... 25 576 settings made for charge 26########################################################################### 27#fix EFIELD all efield $E 0.0 0.0 28########################################################################### 29fix ATC real atc species_electrostatic Ar_species.mat 30ATC: constructing electrostatic species coupling with parameter file Ar_species.mat 31 ATC: version 2.0 32 ATC: peratom PE compute created with ID: 3 33 ATC: WARNING: material units real do not match lammps 34 ATC: 1 materials defined from Ar_species.mat 35 ATC: creating fem_efield extrinsic model 36 ATC: WARNING: material units real do not match lammps 37 ATC: 1 materials defined from Ar_species.mat 38fix_modify ATC add_species ion type 1 ### <<<<< 39#fix_modify ATC add_species REAL group real 40fix_modify ATC include atomic_charge 41fix_modify ATC internal_quadrature off 42fix_modify ATC extrinsic short_range off 43fix_modify ATC mesh create ${nx} 1 1 BOX f p p 44fix_modify ATC mesh create 32 1 1 BOX f p p 45 ATC: created uniform mesh with 132 nodes, 33 unique nodes, and 32 elements 46fix_modify ATC atom_element_map eulerian 1 47fix_modify ATC atom_weight multiscale 48fix_modify ATC initial mass_density all 0. 49#fix_modify ATC initial charge_density all 0. 50########################################################################### 51variable n equal count(real) 52print "number of atoms: $n" 53number of atoms: 576 54timestep 0.0 55thermo 1 56compute Fx real reduce sum fx 57compute Fy real reduce sum fy 58thermo_style custom step etotal temp press pe c_Fx c_Fy 59fix_modify ATC output poissonFE 1 text binary 60 ATC: Warning : text output can create _LARGE_ files 61 ATC: output custom names: 62NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationion 63species_concentration : species_concentrationion 64 65# (1) all fixed 66fix_modify ATC fix electric_potential all linear 0 0 0 $E 0 0 0 0 67fix_modify ATC fix electric_potential all linear 0 0 0 20 0 0 0 0 68 ATC: created function : 0 + 20(x-0)+0(y-0)+0(z-0) 69run 1 70Setting up run ... 71 ATC: WARNING: material: [ar] cannot find mass_density 72 ATC: WARNING: physics model: [species], material: [ar] does not provide all interfaces for <mass_density> physics and will be treated as null 73 ATC: WARNING: all initial conditions for charge_density have not been defined and the undefined are assumed zero 74 ATC: WARNING: all initial conditions for species_concentration have not been defined and the undefined are assumed zero 75 ATC: WARNING: material: [ar] cannot find mass_density 76 ATC: WARNING: physics model: [species electrostatic], material: [ar] does not provide all interfaces for <mass_density> physics and will be treated as null 77Memory usage per processor = 48.9866 Mbytes 78Step TotEng Temp Press PotEng Fx Fy 79 0 13388.811 0 12185513 13388.811 -11520 -5.4091662e-13 80 1 13388.811 0 12185513 13388.811 -11520 -5.4091662e-13 81Loop time of 0.00854391 on 4 procs for 1 steps with 576 atoms 82 83Pair time (%) = 0.00297153 (34.7795) 84Bond time (%) = 7.7486e-07 (0.00906916) 85Neigh time (%) = 0 (0) 86Comm time (%) = 0.000446737 (5.22872) 87Outpt time (%) = 0.00115174 (13.4803) 88Other time (%) = 0.00397313 (46.5024) 89 90Nlocal: 144 ave 144 max 144 min 91Histogram: 4 0 0 0 0 0 0 0 0 0 92Nghost: 3556 ave 4256 max 2856 min 93Histogram: 2 0 0 0 0 0 0 0 0 2 94Neighs: 58212 ave 63792 max 52524 min 95Histogram: 2 0 0 0 0 0 0 0 0 2 96FullNghs: 116424 ave 127584 max 105264 min 97Histogram: 2 0 0 0 0 0 0 0 0 2 98 99Total # of neighbors = 465696 100Ave neighs/atom = 808.5 101Ave special neighs/atom = 0 102Neighbor list builds = 0 103Dangerous builds = 0 104# (2) Dirichlet 105# NOTE with correct density solution is very close 106#fix_modify ATC fix charge_density all 0.0588951459091903 107fix_modify ATC unfix electric_potential all 108fix_modify ATC mesh create_nodeset lbc 0.0 0.0 -INF INF -INF INF 109 ATC: created nodeset lbc with 1 nodes 110fix_modify ATC mesh create_faceset lbc 0.0 INF -INF INF -INF INF 111 ATC: created faceset lbc with 1 faces 112fix_modify ATC mesh create_faceset rbc -INF 16.0 -INF INF -INF INF 113 ATC: created faceset rbc with 1 faces 114fix_modify ATC fix electric_potential lbc 100.0 115run 1 116Setting up run ... 117 ATC: WARNING: material: [ar] cannot find mass_density 118 ATC: WARNING: physics model: [species], material: [ar] does not provide all interfaces for <mass_density> physics and will be treated as null 119 ATC: WARNING: material: [ar] cannot find mass_density 120 ATC: WARNING: physics model: [species electrostatic], material: [ar] does not provide all interfaces for <mass_density> physics and will be treated as null 121Memory usage per processor = 48.9866 Mbytes 122Step TotEng Temp Press PotEng Fx Fy 123 1 13388.811 0 12185513 13388.811 -200361.27 6.719863e-13 124 2 13388.811 0 12185513 13388.811 -200361.27 6.719863e-13 125Loop time of 0.00797898 on 4 procs for 1 steps with 576 atoms 126 127Pair time (%) = 0.00296175 (37.1195) 128Bond time (%) = 2.38419e-07 (0.00298809) 129Neigh time (%) = 0 (0) 130Comm time (%) = 0.000458777 (5.74982) 131Outpt time (%) = 0.000847757 (10.6249) 132Other time (%) = 0.00371045 (46.5028) 133 134Nlocal: 144 ave 144 max 144 min 135Histogram: 4 0 0 0 0 0 0 0 0 0 136Nghost: 3556 ave 4256 max 2856 min 137Histogram: 2 0 0 0 0 0 0 0 0 2 138Neighs: 58212 ave 63792 max 52524 min 139Histogram: 2 0 0 0 0 0 0 0 0 2 140FullNghs: 116424 ave 127584 max 105264 min 141Histogram: 2 0 0 0 0 0 0 0 0 2 142 143Total # of neighbors = 465696 144Ave neighs/atom = 808.5 145Ave special neighs/atom = 0 146Neighbor list builds = 0 147Dangerous builds = 0 148# (3) Neumann 149fix_modify ATC fix_flux electric_potential rbc 0.5 150run 1 151Setting up run ... 152 ATC: WARNING: material: [ar] cannot find mass_density 153 ATC: WARNING: physics model: [species], material: [ar] does not provide all interfaces for <mass_density> physics and will be treated as null 154 ATC: WARNING: material: [ar] cannot find mass_density 155 ATC: WARNING: physics model: [species electrostatic], material: [ar] does not provide all interfaces for <mass_density> physics and will be treated as null 156Memory usage per processor = 48.9866 Mbytes 157Step TotEng Temp Press PotEng Fx Fy 158 2 13388.811 0 12185513 13388.811 -252475.24 1.1650611e-12 159 3 13388.811 0 12185513 13388.811 -252475.24 1.1650611e-12 160Loop time of 0.00814193 on 4 procs for 1 steps with 576 atoms 161 162Pair time (%) = 0.0029577 (36.3268) 163Bond time (%) = 2.98023e-07 (0.00366035) 164Neigh time (%) = 0 (0) 165Comm time (%) = 0.000454485 (5.58203) 166Outpt time (%) = 0.000847459 (10.4086) 167Other time (%) = 0.00388199 (47.679) 168 169Nlocal: 144 ave 144 max 144 min 170Histogram: 4 0 0 0 0 0 0 0 0 0 171Nghost: 3556 ave 4256 max 2856 min 172Histogram: 2 0 0 0 0 0 0 0 0 2 173Neighs: 58212 ave 63792 max 52524 min 174Histogram: 2 0 0 0 0 0 0 0 0 2 175FullNghs: 116424 ave 127584 max 105264 min 176Histogram: 2 0 0 0 0 0 0 0 0 2 177 178Total # of neighbors = 465696 179Ave neighs/atom = 808.5 180Ave special neighs/atom = 0 181Neighbor list builds = 0 182Dangerous builds = 0 183# (4) Robin eps_1 phi'_1 = eps_2/L_2 (phi_{L_2} - phi) 184fix_modify ATC unfix_flux electric_potential rbc 185fix_modify ATC fix_robin electric_potential rbc 0.5 -0.00001 186 ATC: created function : 0.5 + -1e-05*u 187run 1 188Setting up run ... 189 ATC: WARNING: material: [ar] cannot find mass_density 190 ATC: WARNING: physics model: [species], material: [ar] does not provide all interfaces for <mass_density> physics and will be treated as null 191 ATC: WARNING: material: [ar] cannot find mass_density 192 ATC: WARNING: physics model: [species electrostatic], material: [ar] does not provide all interfaces for <mass_density> physics and will be treated as null 193Memory usage per processor = 48.9866 Mbytes 194Step TotEng Temp Press PotEng Fx Fy 195 3 13388.811 0 12185513 13388.811 -225709.12 9.1181426e-13 196 4 13388.811 0 12185513 13388.811 -225709.12 9.1181426e-13 197Loop time of 0.00825572 on 4 procs for 1 steps with 576 atoms 198 199Pair time (%) = 0.00296426 (35.9055) 200Bond time (%) = 7.15256e-07 (0.00866376) 201Neigh time (%) = 0 (0) 202Comm time (%) = 0.000457525 (5.54192) 203Outpt time (%) = 0.000843704 (10.2196) 204Other time (%) = 0.00398952 (48.3243) 205 206Nlocal: 144 ave 144 max 144 min 207Histogram: 4 0 0 0 0 0 0 0 0 0 208Nghost: 3556 ave 4256 max 2856 min 209Histogram: 2 0 0 0 0 0 0 0 0 2 210Neighs: 58212 ave 63792 max 52524 min 211Histogram: 2 0 0 0 0 0 0 0 0 2 212FullNghs: 116424 ave 127584 max 105264 min 213Histogram: 2 0 0 0 0 0 0 0 0 2 214 215Total # of neighbors = 465696 216Ave neighs/atom = 808.5 217Ave special neighs/atom = 0 218Neighbor list builds = 0 219Dangerous builds = 0 220# (5) Robins on the left and Robins on the right 221fix_modify ATC unfix electric_potential lbc 222fix_modify ATC fix_robin electric_potential rbc 0.01 -0.0001 223 ATC: created function : 0.01 + -0.0001*u 224fix_modify ATC fix_robin electric_potential lbc 0.01 -0.0001 225 ATC: created function : 0.01 + -0.0001*u 226run 1 227Setting up run ... 228 ATC: WARNING: material: [ar] cannot find mass_density 229 ATC: WARNING: physics model: [species], material: [ar] does not provide all interfaces for <mass_density> physics and will be treated as null 230 ATC: WARNING: material: [ar] cannot find mass_density 231 ATC: WARNING: physics model: [species electrostatic], material: [ar] does not provide all interfaces for <mass_density> physics and will be treated as null 232Memory usage per processor = 48.9866 Mbytes 233Step TotEng Temp Press PotEng Fx Fy 234 4 13388.811 0 12185513 13388.811 4.3291948e-09 -1.4571568e-12 235 5 13388.811 0 12185513 13388.811 4.3364707e-09 -1.4571568e-12 236Loop time of 0.00868404 on 4 procs for 1 steps with 576 atoms 237 238Pair time (%) = 0.00308079 (35.4764) 239Bond time (%) = 2.38419e-07 (0.00274548) 240Neigh time (%) = 0 (0) 241Comm time (%) = 0.000677586 (7.80265) 242Outpt time (%) = 0.000885546 (10.1974) 243Other time (%) = 0.00403988 (46.5208) 244 245Nlocal: 144 ave 144 max 144 min 246Histogram: 4 0 0 0 0 0 0 0 0 0 247Nghost: 3556 ave 4256 max 2856 min 248Histogram: 2 0 0 0 0 0 0 0 0 2 249Neighs: 58212 ave 63792 max 52524 min 250Histogram: 2 0 0 0 0 0 0 0 0 2 251FullNghs: 116424 ave 127584 max 105264 min 252Histogram: 2 0 0 0 0 0 0 0 0 2 253 254Total # of neighbors = 465696 255Ave neighs/atom = 808.5 256Ave special neighs/atom = 0 257Neighbor list builds = 0 258Dangerous builds = 0 259#fix_modify ATC fix charge_density all 0.0 260#run 1 261