LAMMPS (18 Jun 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task # The units we assume we'll use. The kim-lammps-preprocessor # may swap this line out if running against a Simulator Model # whose units are not 'metal' units metal # Variables that can be adjusted by kim-lammps-preprocessor # to switch unit sets for Simulator Models variable _u_distance equal 1.0 variable _u_energy equal 1.0 variable _u_time equal 1.0 variable _u_pressure equal 1.0 variable _u_temperature equal 1.0 dimension 3 # This line may be swapped out by kim-lammps-preprocessor if # running against a Simulator Model whose atom_style is not # 'atomic' atom_style atomic boundary p p p # Set neighbor skin variable neigh_skin equal 2.0*${_u_distance} variable neigh_skin equal 2.0*1 neighbor ${neigh_skin} bin neighbor 2 bin # Atom definition variable latparam_converted equal 4.0505223214626325*${_u_distance} variable latparam_converted equal 4.0505223214626325*1 # Declare the dimensions of the model in lattice cells variable nlat_x equal 1 variable nlat_y equal 1 variable nlat_z equal 58 # Define the box/various dimensions. Start with x and y dimensions. # Before converting to the active unit set, get their value in Angstroms # for later normalization variable xdim equal (4.0505223214626325*sqrt(6)/2)*${nlat_x} variable xdim equal (4.0505223214626325*sqrt(6)/2)*1 variable ydim equal (4.0505223214626325*sqrt(2)/2)*${nlat_y} variable ydim equal (4.0505223214626325*sqrt(2)/2)*1 # Area of the stacking fault plane in Angstrom^2 variable Area equal 2*${xdim}*${ydim} variable Area equal 2*4.96085643966851*${ydim} variable Area equal 2*4.96085643966851*2.8641518008537 # Now convert xdim and ydim to the active unit set and do z direction variable xdim equal ${xdim}*${_u_distance} variable xdim equal 4.96085643966851*${_u_distance} variable xdim equal 4.96085643966851*1 variable ydim equal ${ydim}*${_u_distance} variable ydim equal 2.8641518008537*${_u_distance} variable ydim equal 2.8641518008537*1 variable zdim equal (${latparam_converted}/sqrt(3))*${nlat_z} variable zdim equal (4.05052232146263/sqrt(3))*${nlat_z} variable zdim equal (4.05052232146263/sqrt(3))*58 variable layer_z equal (${latparam_converted}/sqrt(3)) variable layer_z equal (4.05052232146263/sqrt(3)) # Geometry definition lattice fcc ${latparam_converted} lattice fcc 4.05052232146263 Lattice spacing in x,y,z = 4.05052 4.05052 4.05052 # Define regions for stacking fault test # NOTE: -0.001 in the x- and y- directions only to overcome numerical # precision issues (no need to worry about units on these quantities) # Define a region for each of the top N_layers/2 variable ntwin_layers equal ${nlat_z}/2 variable ntwin_layers equal 58/2 variable i loop ${ntwin_layers} variable i loop 29 label start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 1+${ntwin_layers} variable j equal 1+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (30-1.0)*${layer_z}-0.001 variable zmin equal (30-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 30*${layer_z}-0.001 variable zmax equal 30*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 1 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 1 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 1 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 1 block -0.001 4.96085643966851 -0.001 2.8641518008537 67.8175344269962 ${zmax} units box region 1 block -0.001 4.96085643966851 -0.001 2.8641518008537 67.8175344269962 70.1561045796512 units box next i jump SELF start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 2+${ntwin_layers} variable j equal 2+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (31-1.0)*${layer_z}-0.001 variable zmin equal (31-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 31*${layer_z}-0.001 variable zmax equal 31*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 2 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 2 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 2 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 2 block -0.001 4.96085643966851 -0.001 2.8641518008537 70.1561045796512 ${zmax} units box region 2 block -0.001 4.96085643966851 -0.001 2.8641518008537 70.1561045796512 72.4946747323062 units box next i jump SELF start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 3+${ntwin_layers} variable j equal 3+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (32-1.0)*${layer_z}-0.001 variable zmin equal (32-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 32*${layer_z}-0.001 variable zmax equal 32*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 3 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 3 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 3 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 3 block -0.001 4.96085643966851 -0.001 2.8641518008537 72.4946747323062 ${zmax} units box region 3 block -0.001 4.96085643966851 -0.001 2.8641518008537 72.4946747323062 74.8332448849613 units box next i jump SELF start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 4+${ntwin_layers} variable j equal 4+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (33-1.0)*${layer_z}-0.001 variable zmin equal (33-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 33*${layer_z}-0.001 variable zmax equal 33*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 4 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 4 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 4 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 4 block -0.001 4.96085643966851 -0.001 2.8641518008537 74.8332448849613 ${zmax} units box region 4 block -0.001 4.96085643966851 -0.001 2.8641518008537 74.8332448849613 77.1718150376163 units box next i jump SELF start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 5+${ntwin_layers} variable j equal 5+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (34-1.0)*${layer_z}-0.001 variable zmin equal (34-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 34*${layer_z}-0.001 variable zmax equal 34*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 5 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 5 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 5 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 5 block -0.001 4.96085643966851 -0.001 2.8641518008537 77.1718150376163 ${zmax} units box region 5 block -0.001 4.96085643966851 -0.001 2.8641518008537 77.1718150376163 79.5103851902714 units box next i jump SELF start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 6+${ntwin_layers} variable j equal 6+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (35-1.0)*${layer_z}-0.001 variable zmin equal (35-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 35*${layer_z}-0.001 variable zmax equal 35*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 6 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 6 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 6 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 6 block -0.001 4.96085643966851 -0.001 2.8641518008537 79.5103851902714 ${zmax} units box region 6 block -0.001 4.96085643966851 -0.001 2.8641518008537 79.5103851902714 81.8489553429264 units box next i jump SELF start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 7+${ntwin_layers} variable j equal 7+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (36-1.0)*${layer_z}-0.001 variable zmin equal (36-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 36*${layer_z}-0.001 variable zmax equal 36*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 7 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 7 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 7 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 7 block -0.001 4.96085643966851 -0.001 2.8641518008537 81.8489553429264 ${zmax} units box region 7 block -0.001 4.96085643966851 -0.001 2.8641518008537 81.8489553429264 84.1875254955814 units box next i jump SELF start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 8+${ntwin_layers} variable j equal 8+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (37-1.0)*${layer_z}-0.001 variable zmin equal (37-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 37*${layer_z}-0.001 variable zmax equal 37*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 8 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 8 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 8 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 8 block -0.001 4.96085643966851 -0.001 2.8641518008537 84.1875254955814 ${zmax} units box region 8 block -0.001 4.96085643966851 -0.001 2.8641518008537 84.1875254955814 86.5260956482365 units box next i jump SELF start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 9+${ntwin_layers} variable j equal 9+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (38-1.0)*${layer_z}-0.001 variable zmin equal (38-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 38*${layer_z}-0.001 variable zmax equal 38*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 9 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 9 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 9 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 9 block -0.001 4.96085643966851 -0.001 2.8641518008537 86.5260956482365 ${zmax} units box region 9 block -0.001 4.96085643966851 -0.001 2.8641518008537 86.5260956482365 88.8646658008915 units box next i jump SELF start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 10+${ntwin_layers} variable j equal 10+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (39-1.0)*${layer_z}-0.001 variable zmin equal (39-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 39*${layer_z}-0.001 variable zmax equal 39*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 10 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 10 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 10 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 10 block -0.001 4.96085643966851 -0.001 2.8641518008537 88.8646658008915 ${zmax} units box region 10 block -0.001 4.96085643966851 -0.001 2.8641518008537 88.8646658008915 91.2032359535466 units box next i jump SELF start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 11+${ntwin_layers} variable j equal 11+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (40-1.0)*${layer_z}-0.001 variable zmin equal (40-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 40*${layer_z}-0.001 variable zmax equal 40*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 11 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 11 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 11 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 11 block -0.001 4.96085643966851 -0.001 2.8641518008537 91.2032359535466 ${zmax} units box region 11 block -0.001 4.96085643966851 -0.001 2.8641518008537 91.2032359535466 93.5418061062016 units box next i jump SELF start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 12+${ntwin_layers} variable j equal 12+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (41-1.0)*${layer_z}-0.001 variable zmin equal (41-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 41*${layer_z}-0.001 variable zmax equal 41*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 12 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 12 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 12 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 12 block -0.001 4.96085643966851 -0.001 2.8641518008537 93.5418061062016 ${zmax} units box region 12 block -0.001 4.96085643966851 -0.001 2.8641518008537 93.5418061062016 95.8803762588566 units box next i jump SELF start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 13+${ntwin_layers} variable j equal 13+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (42-1.0)*${layer_z}-0.001 variable zmin equal (42-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 42*${layer_z}-0.001 variable zmax equal 42*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 13 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 13 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 13 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 13 block -0.001 4.96085643966851 -0.001 2.8641518008537 95.8803762588566 ${zmax} units box region 13 block -0.001 4.96085643966851 -0.001 2.8641518008537 95.8803762588566 98.2189464115117 units box next i jump SELF start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 14+${ntwin_layers} variable j equal 14+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (43-1.0)*${layer_z}-0.001 variable zmin equal (43-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 43*${layer_z}-0.001 variable zmax equal 43*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 14 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 14 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 14 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 14 block -0.001 4.96085643966851 -0.001 2.8641518008537 98.2189464115117 ${zmax} units box region 14 block -0.001 4.96085643966851 -0.001 2.8641518008537 98.2189464115117 100.557516564167 units box next i jump SELF start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 15+${ntwin_layers} variable j equal 15+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (44-1.0)*${layer_z}-0.001 variable zmin equal (44-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 44*${layer_z}-0.001 variable zmax equal 44*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 15 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 15 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 15 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 15 block -0.001 4.96085643966851 -0.001 2.8641518008537 100.557516564167 ${zmax} units box region 15 block -0.001 4.96085643966851 -0.001 2.8641518008537 100.557516564167 102.896086716822 units box next i jump SELF start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 16+${ntwin_layers} variable j equal 16+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (45-1.0)*${layer_z}-0.001 variable zmin equal (45-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 45*${layer_z}-0.001 variable zmax equal 45*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 16 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 16 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 16 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 16 block -0.001 4.96085643966851 -0.001 2.8641518008537 102.896086716822 ${zmax} units box region 16 block -0.001 4.96085643966851 -0.001 2.8641518008537 102.896086716822 105.234656869477 units box next i jump SELF start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 17+${ntwin_layers} variable j equal 17+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (46-1.0)*${layer_z}-0.001 variable zmin equal (46-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 46*${layer_z}-0.001 variable zmax equal 46*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 17 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 17 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 17 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 17 block -0.001 4.96085643966851 -0.001 2.8641518008537 105.234656869477 ${zmax} units box region 17 block -0.001 4.96085643966851 -0.001 2.8641518008537 105.234656869477 107.573227022132 units box next i jump SELF start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 18+${ntwin_layers} variable j equal 18+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (47-1.0)*${layer_z}-0.001 variable zmin equal (47-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 47*${layer_z}-0.001 variable zmax equal 47*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 18 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 18 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 18 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 18 block -0.001 4.96085643966851 -0.001 2.8641518008537 107.573227022132 ${zmax} units box region 18 block -0.001 4.96085643966851 -0.001 2.8641518008537 107.573227022132 109.911797174787 units box next i jump SELF start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 19+${ntwin_layers} variable j equal 19+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (48-1.0)*${layer_z}-0.001 variable zmin equal (48-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 48*${layer_z}-0.001 variable zmax equal 48*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 19 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 19 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 19 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 19 block -0.001 4.96085643966851 -0.001 2.8641518008537 109.911797174787 ${zmax} units box region 19 block -0.001 4.96085643966851 -0.001 2.8641518008537 109.911797174787 112.250367327442 units box next i jump SELF start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 20+${ntwin_layers} variable j equal 20+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (49-1.0)*${layer_z}-0.001 variable zmin equal (49-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 49*${layer_z}-0.001 variable zmax equal 49*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 20 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 20 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 20 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 20 block -0.001 4.96085643966851 -0.001 2.8641518008537 112.250367327442 ${zmax} units box region 20 block -0.001 4.96085643966851 -0.001 2.8641518008537 112.250367327442 114.588937480097 units box next i jump SELF start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 21+${ntwin_layers} variable j equal 21+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (50-1.0)*${layer_z}-0.001 variable zmin equal (50-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 50*${layer_z}-0.001 variable zmax equal 50*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 21 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 21 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 21 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 21 block -0.001 4.96085643966851 -0.001 2.8641518008537 114.588937480097 ${zmax} units box region 21 block -0.001 4.96085643966851 -0.001 2.8641518008537 114.588937480097 116.927507632752 units box next i jump SELF start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 22+${ntwin_layers} variable j equal 22+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (51-1.0)*${layer_z}-0.001 variable zmin equal (51-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 51*${layer_z}-0.001 variable zmax equal 51*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 22 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 22 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 22 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 22 block -0.001 4.96085643966851 -0.001 2.8641518008537 116.927507632752 ${zmax} units box region 22 block -0.001 4.96085643966851 -0.001 2.8641518008537 116.927507632752 119.266077785407 units box next i jump SELF start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 23+${ntwin_layers} variable j equal 23+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (52-1.0)*${layer_z}-0.001 variable zmin equal (52-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 52*${layer_z}-0.001 variable zmax equal 52*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 23 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 23 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 23 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 23 block -0.001 4.96085643966851 -0.001 2.8641518008537 119.266077785407 ${zmax} units box region 23 block -0.001 4.96085643966851 -0.001 2.8641518008537 119.266077785407 121.604647938062 units box next i jump SELF start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 24+${ntwin_layers} variable j equal 24+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (53-1.0)*${layer_z}-0.001 variable zmin equal (53-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 53*${layer_z}-0.001 variable zmax equal 53*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 24 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 24 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 24 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 24 block -0.001 4.96085643966851 -0.001 2.8641518008537 121.604647938062 ${zmax} units box region 24 block -0.001 4.96085643966851 -0.001 2.8641518008537 121.604647938062 123.943218090717 units box next i jump SELF start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 25+${ntwin_layers} variable j equal 25+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (54-1.0)*${layer_z}-0.001 variable zmin equal (54-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 54*${layer_z}-0.001 variable zmax equal 54*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 25 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 25 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 25 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 25 block -0.001 4.96085643966851 -0.001 2.8641518008537 123.943218090717 ${zmax} units box region 25 block -0.001 4.96085643966851 -0.001 2.8641518008537 123.943218090717 126.281788243372 units box next i jump SELF start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 26+${ntwin_layers} variable j equal 26+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (55-1.0)*${layer_z}-0.001 variable zmin equal (55-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 55*${layer_z}-0.001 variable zmax equal 55*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 26 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 26 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 26 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 26 block -0.001 4.96085643966851 -0.001 2.8641518008537 126.281788243372 ${zmax} units box region 26 block -0.001 4.96085643966851 -0.001 2.8641518008537 126.281788243372 128.620358396027 units box next i jump SELF start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 27+${ntwin_layers} variable j equal 27+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (56-1.0)*${layer_z}-0.001 variable zmin equal (56-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 56*${layer_z}-0.001 variable zmax equal 56*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 27 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 27 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 27 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 27 block -0.001 4.96085643966851 -0.001 2.8641518008537 128.620358396027 ${zmax} units box region 27 block -0.001 4.96085643966851 -0.001 2.8641518008537 128.620358396027 130.958928548682 units box next i jump SELF start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 28+${ntwin_layers} variable j equal 28+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (57-1.0)*${layer_z}-0.001 variable zmin equal (57-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 57*${layer_z}-0.001 variable zmax equal 57*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 28 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 28 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 28 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 28 block -0.001 4.96085643966851 -0.001 2.8641518008537 130.958928548682 ${zmax} units box region 28 block -0.001 4.96085643966851 -0.001 2.8641518008537 130.958928548682 133.297498701337 units box next i jump SELF start_of_loop_region variable j equal ${i}+${ntwin_layers} variable j equal 29+${ntwin_layers} variable j equal 29+29 variable zmin equal (${j}-1.0)*${layer_z}-0.001 variable zmin equal (58-1.0)*${layer_z}-0.001 variable zmin equal (58-1.0)*2.33857015265504-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 58*${layer_z}-0.001 variable zmax equal 58*2.33857015265504-0.001 region ${i} block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 29 block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region 29 block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region 29 block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region 29 block -0.001 4.96085643966851 -0.001 2.8641518008537 133.297498701337 ${zmax} units box region 29 block -0.001 4.96085643966851 -0.001 2.8641518008537 133.297498701337 135.636068853992 units box next i jump SELF start_of_loop_region variable i delete variable j delete # Declare group for the rigid blocks for intrinsic stacking fault variable zmin equal (15-1.0)*${layer_z}-0.001 variable zmin equal (15-1.0)*2.33857015265504-0.001 variable zmax equal (45-1.0)*${layer_z}+0.001 variable zmax equal (45-1.0)*2.33857015265504+0.001 region stack_region block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region stack_region block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region stack_region block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region stack_region block -0.001 4.96085643966851 -0.001 2.8641518008537 32.7389821371706 ${zmax} units box region stack_region block -0.001 4.96085643966851 -0.001 2.8641518008537 32.7389821371706 102.898086716822 units box # Declare group for the rigid blocks for the extrisic stacking fault variable zmin equal (16-1.0)*${layer_z}-0.001 variable zmin equal (16-1.0)*2.33857015265504-0.001 variable zmax equal (44-1.0)*${layer_z}+0.001 variable zmax equal (44-1.0)*2.33857015265504+0.001 region twin_region block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region twin_region block -0.001 4.96085643966851 -0.001 ${ydim} ${zmin} ${zmax} units box region twin_region block -0.001 4.96085643966851 -0.001 2.8641518008537 ${zmin} ${zmax} units box region twin_region block -0.001 4.96085643966851 -0.001 2.8641518008537 35.0775522898256 ${zmax} units box region twin_region block -0.001 4.96085643966851 -0.001 2.8641518008537 35.0775522898256 100.559516564167 units box # Create simulation box and atoms region whole block 0-0.001 ${xdim}+0.001 0-0.001 ${ydim}+0.001 0-0.001 ${zdim}+0.001 units box region whole block 0-0.001 4.96085643966851+0.001 0-0.001 ${ydim}+0.001 0-0.001 ${zdim}+0.001 units box region whole block 0-0.001 4.96085643966851+0.001 0-0.001 2.8641518008537+0.001 0-0.001 ${zdim}+0.001 units box region whole block 0-0.001 4.96085643966851+0.001 0-0.001 2.8641518008537+0.001 0-0.001 135.637068853992+0.001 units box create_box 1 whole Created orthogonal box = (0 0 0) to (4.96086 2.86415 135.637) 1 by 1 by 1 MPI processor grid lattice fcc ${latparam_converted} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 lattice fcc 4.05052232146263 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 Lattice spacing in x,y,z = 6.61448 5.7283 7.01571 create_atoms 1 region whole Created 116 atoms create_atoms CPU = 0.000663996 secs # Define the interatomic potentials pair_style kim Morse_EIP_GuthikondaElliott_2011_AuCd__MO_703849496106_002 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1089) pair_coeff * * Au mass * 1.0 # Rigid holding settings for each layer as a group variable i loop ${ntwin_layers} variable i loop 29 label start_of_loop_group group ${i} region ${i} group 1 region ${i} group 1 region 1 2 atoms in group 1 next i jump SELF start_of_loop_group group ${i} region ${i} group 2 region ${i} group 2 region 2 2 atoms in group 2 next i jump SELF start_of_loop_group group ${i} region ${i} group 3 region ${i} group 3 region 3 2 atoms in group 3 next i jump SELF start_of_loop_group group ${i} region ${i} group 4 region ${i} group 4 region 4 2 atoms in group 4 next i jump SELF start_of_loop_group group ${i} region ${i} group 5 region ${i} group 5 region 5 2 atoms in group 5 next i jump SELF start_of_loop_group group ${i} region ${i} group 6 region ${i} group 6 region 6 2 atoms in group 6 next i jump SELF start_of_loop_group group ${i} region ${i} group 7 region ${i} group 7 region 7 2 atoms in group 7 next i jump SELF start_of_loop_group group ${i} region ${i} group 8 region ${i} group 8 region 8 2 atoms in group 8 next i jump SELF start_of_loop_group group ${i} region ${i} group 9 region ${i} group 9 region 9 2 atoms in group 9 next i jump SELF start_of_loop_group group ${i} region ${i} group 10 region ${i} group 10 region 10 2 atoms in group 10 next i jump SELF start_of_loop_group group ${i} region ${i} group 11 region ${i} group 11 region 11 2 atoms in group 11 next i jump SELF start_of_loop_group group ${i} region ${i} group 12 region ${i} group 12 region 12 2 atoms in group 12 next i jump SELF start_of_loop_group group ${i} region ${i} group 13 region ${i} group 13 region 13 2 atoms in group 13 next i jump SELF start_of_loop_group group ${i} region ${i} group 14 region ${i} group 14 region 14 2 atoms in group 14 next i jump SELF start_of_loop_group group ${i} region ${i} group 15 region ${i} group 15 region 15 2 atoms in group 15 next i jump SELF start_of_loop_group group ${i} region ${i} group 16 region ${i} group 16 region 16 2 atoms in group 16 next i jump SELF start_of_loop_group group ${i} region ${i} group 17 region ${i} group 17 region 17 2 atoms in group 17 next i jump SELF start_of_loop_group group ${i} region ${i} group 18 region ${i} group 18 region 18 2 atoms in group 18 next i jump SELF start_of_loop_group group ${i} region ${i} group 19 region ${i} group 19 region 19 2 atoms in group 19 next i jump SELF start_of_loop_group group ${i} region ${i} group 20 region ${i} group 20 region 20 2 atoms in group 20 next i jump SELF start_of_loop_group group ${i} region ${i} group 21 region ${i} group 21 region 21 2 atoms in group 21 next i jump SELF start_of_loop_group group ${i} region ${i} group 22 region ${i} group 22 region 22 2 atoms in group 22 next i jump SELF start_of_loop_group group ${i} region ${i} group 23 region ${i} group 23 region 23 2 atoms in group 23 next i jump SELF start_of_loop_group group ${i} region ${i} group 24 region ${i} group 24 region 24 2 atoms in group 24 next i jump SELF start_of_loop_group group ${i} region ${i} group 25 region ${i} group 25 region 25 2 atoms in group 25 next i jump SELF start_of_loop_group group ${i} region ${i} group 26 region ${i} group 26 region 26 2 atoms in group 26 next i jump SELF start_of_loop_group group ${i} region ${i} group 27 region ${i} group 27 region 27 2 atoms in group 27 next i jump SELF start_of_loop_group group ${i} region ${i} group 28 region ${i} group 28 region 28 2 atoms in group 28 next i jump SELF start_of_loop_group group ${i} region ${i} group 29 region ${i} group 29 region 29 2 atoms in group 29 next i jump SELF start_of_loop_group variable i delete # Rigid holding settings for the stacking fault group group stack_group region stack_region 62 atoms in group stack_group # Rigid holding settings for the twinning fault group group twin_group region twin_region 58 atoms in group twin_group # Variables used to rescale the energy and stress so that the quantities # in the thermo output are in the original metal units (eV and bars) # even if we're running with a Simulator Model that uses different units variable pe_metal equal "c_thermo_pe/v__u_energy" variable press_metal equal "c_thermo_press/v__u_pressure" variable pxx_metal equal pxx/${_u_pressure} variable pxx_metal equal pxx/1 variable pyy_metal equal pyy/${_u_pressure} variable pyy_metal equal pyy/1 variable pzz_metal equal pzz/${_u_pressure} variable pzz_metal equal pzz/1 variable temp_metal equal temp/${_u_temperature} variable temp_metal equal temp/1 # Compute initial energy and output thermo 100 thermo_style custom step v_pe_metal press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal temp v_temp_metal #dump config all atom 1000 dump.Stack # Perform initial relaxation reset_timestep 0 fix 1 all box/relax x 0.0 y 0.0 z 0.0 vmax 0.01 min_style cg minimize 1e-25 1e-25 10000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 22 ghost atom cutoff = 22 binsize = 11, bins = 1 1 13 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 22 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard ERROR on proc 0: Neighbor list overflow, boost neigh_modify one (src/npair_full_bin_atomonly.cpp:90) Last command: minimize 1e-25 1e-25 10000 10000