LAMMPS (30 Aug 2013) units metal variable s equal 100 variable T equal 20 variable n equal 0.000004 variable tol equal 0.1 variable W equal 1000 atom_style atomic lattice fcc 5.405 origin 0.25 0.25 0.25 Lattice spacing in x,y,z = 5.405 5.405 5.405 region FE block -8 8 -6 6 0 3 region MD block -7 7 -6 0 0 3 region FREE block -4 4 -6 0 0 3 boundary f f p # create atoms create_box 1 FE Created orthogonal box = (-43.24 -32.43 0) to (43.24 32.43 16.215) 2 by 2 by 1 MPI processor grid mass 1 39.95 atom_modify sort 0 1 timestep 0.002 thermo $s thermo 100 # ID group atc PhysicsType ParameterFile fix AtC all atc drift_diffusion Ar_ddm.mat ATC: constructing drift_diffusion coupling with parameter file Ar_ddm.mat ATC: version 2.0 ATC: peratom PE compute created with ID: 3 ATC: WARNING: material units real do not match lammps ATC: WARNING: material units real do not match lammps ATC: 2 materials defined from Ar_ddm.mat ATC: creating drift_diffusion extrinsic model ATC: WARNING: material units real do not match lammps ATC: WARNING: material units real do not match lammps ATC: 2 materials defined from Ar_ddm.mat ATC: WARNING: material units real do not match lammps ATC: WARNING: material units real do not match lammps ATC: 2 materials defined from Ar_ddm.mat # ID part keywords nx ny nz region fix_modify AtC mesh create 4 4 1 FE f f p ATC: created uniform mesh with 50 nodes, 25 unique nodes, and 16 elements variable a equal $W+${tol} variable a equal 1000+${tol} variable a equal 1000+0.10000000000000000555 fix_modify AtC mesh create_elementset wire -$a $a -INF ${tol} -INF INF fix_modify AtC mesh create_elementset wire -1000.1000000000000227 $a -INF ${tol} -INF INF fix_modify AtC mesh create_elementset wire -1000.1000000000000227 1000.1000000000000227 -INF ${tol} -INF INF fix_modify AtC mesh create_elementset wire -1000.1000000000000227 1000.1000000000000227 -INF 0.10000000000000000555 -INF INF ATC: created elementset wire with 8 elements fix_modify AtC mesh create_elementset gap -$a $a -${tol} INF -INF INF fix_modify AtC mesh create_elementset gap -1000.1000000000000227 $a -${tol} INF -INF INF fix_modify AtC mesh create_elementset gap -1000.1000000000000227 1000.1000000000000227 -${tol} INF -INF INF fix_modify AtC mesh create_elementset gap -1000.1000000000000227 1000.1000000000000227 -0.10000000000000000555 INF -INF INF ATC: created elementset gap with 8 elements # void is the complement of the wire nodeset variable a equal $W-${tol} variable a equal 1000-${tol} variable a equal 1000-0.10000000000000000555 fix_modify AtC mesh create_nodeset void -$a $a ${tol} INF -INF INF fix_modify AtC mesh create_nodeset void -999.89999999999997726 $a ${tol} INF -INF INF fix_modify AtC mesh create_nodeset void -999.89999999999997726 999.89999999999997726 ${tol} INF -INF INF fix_modify AtC mesh create_nodeset void -999.89999999999997726 999.89999999999997726 0.10000000000000000555 INF -INF INF ATC: created nodeset void with 10 nodes fix_modify AtC mesh output null_material_ddmMESH binary fix_modify AtC control thermal none # fix a temperature fix_modify AtC initial temperature all $T fix_modify AtC initial temperature all 20 fix_modify AtC initial electron_temperature all $T fix_modify AtC initial electron_temperature all 20 fix_modify AtC initial electron_density all $n fix_modify AtC initial electron_density all 3.999999999999999819e-06 fix_modify AtC initial electric_potential all 0.0 fix_modify AtC initial temperature void 0.0 fix_modify AtC initial electron_density void 0.0 fix_modify AtC initial electric_potential void 0.0 # create vacuum fix_modify AtC material gap Vacuum thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] fix_modify AtC output null_material_ddmFE $s full_text binary fix_modify AtC output null_material_ddmFE 100 full_text binary ATC: Warning : text output can create _LARGE_ files ATC: output custom names: fix_modify AtC extrinsic electron_integration implicit # fix_modify AtC mesh create_nodeset lbc -8.1 -7.9 -INF INF -INF INF ATC: created nodeset lbc with 5 nodes fix_modify AtC mesh create_nodeset rbc 7.9 8.1 -INF INF -INF INF ATC: created nodeset rbc with 5 nodes fix_modify AtC fix electron_temperature lbc $T fix_modify AtC fix electron_temperature lbc 20 fix_modify AtC fix electron_temperature rbc $T fix_modify AtC fix electron_temperature rbc 20 fix_modify AtC fix electron_density lbc $n fix_modify AtC fix electron_density lbc 3.999999999999999819e-06 fix_modify AtC fix electric_potential lbc 0.0 variable m equal $s*10 variable m equal 100*10 run $m run 1000 Setting up run ... ATC: WARNING: material: [vacuum] cannot find heat_flux ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null ATC: WARNING: material: [vacuum] cannot find electron_phonon_exchange ATC: WARNING: physics model: [drift-diffusion], material: [vacuum] does not provide all interfaces for physics and will be treated as null ATC: WARNING: material: [vacuum] cannot find electron_flux ATC: WARNING: physics model: [drift-diffusion], material: [vacuum] does not provide all interfaces for physics and will be treated as null ATC: WARNING: material: [vacuum] cannot find electron_heat_capacity ATC: WARNING: physics model: [drift-diffusion], material: [vacuum] does not provide all interfaces for physics and will be treated as null Memory usage per processor = 0.432121 Mbytes Step CPU AtC[1] AtC[2] AtC[3] AtC[4] 0 0 94.264519 12 94.264519 20 100 1.026444 94.267978 12.000392 94.299245 20.003477 200 2.031791 94.276498 12.001352 94.329947 20.006513 300 3.033854 94.289291 12.002784 94.363814 20.009841 400 4.0406649 94.306379 12.004683 94.403041 20.013675 500 5.0435619 94.328129 12.007084 94.449527 20.018196 600 6.0397751 94.355216 12.010055 94.505534 20.023614 700 7.0427639 94.388659 12.0137 94.573962 20.030199 800 8.0464909 94.429901 12.01817 94.65867 20.03831 900 9.0695961 94.480951 12.023673 94.764998 20.048448 1000 10.076592 94.544631 12.030506 94.900724 20.061365 Loop time of 10.0776 on 4 procs for 1000 steps with 0 atoms Pair time (%) = 0 (0) Neigh time (%) = 0 (0) Comm time (%) = 0.00094372 (0.00936449) Outpt time (%) = 0.0274817 (0.272699) Other time (%) = 10.0492 (99.7179) Nlocal: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 0 Neighbor list builds = 0 Dangerous builds = 0