LAMMPS (8 Feb 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) using 1 OpenMP thread(s) per MPI task # Initialize the problem units metal dimension 3 boundary p p p atom_style atomic variable latparam equal 1.59529978037 # 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 variable xdim equal (${latparam}*sqrt(6)/2)*${nlat_x} variable xdim equal (1.59529978037*sqrt(6)/2)*${nlat_x} variable xdim equal (1.59529978037*sqrt(6)/2)*1 variable ydim equal (${latparam}*sqrt(2)/2)*${nlat_y} variable ydim equal (1.59529978037*sqrt(2)/2)*${nlat_y} variable ydim equal (1.59529978037*sqrt(2)/2)*1 variable zdim equal (${latparam}/sqrt(3))*${nlat_z} variable zdim equal (1.59529978037/sqrt(3))*${nlat_z} variable zdim equal (1.59529978037/sqrt(3))*58 variable layer_z equal (${latparam}/sqrt(3)) variable layer_z equal (1.59529978037/sqrt(3)) # Area of the stacking fault plane in Angstrom^2 variable Area equal 2*${xdim}*${ydim} variable Area equal 2*1.95383522434029*${ydim} variable Area equal 2*1.95383522434029*1.12804729272504 # Geometry definition lattice fcc ${latparam} lattice fcc 1.59529978037 Lattice spacing in x,y,z = 1.5953 1.5953 1.5953 # Define regions for stacking fault test # NOTE: -0.001 in the x- and y- directions only to overcome numerical precision issues # 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 30*${layer_z}-0.001 variable zmax equal 30*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 1 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 1 block -0.001 1.95383522434029 -0.001 1.12804729272504 26.7093559714083 ${zmax} units box region 1 block -0.001 1.95383522434029 -0.001 1.12804729272504 26.7093559714083 27.6304027290431 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 31*${layer_z}-0.001 variable zmax equal 31*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 2 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 2 block -0.001 1.95383522434029 -0.001 1.12804729272504 27.6304027290431 ${zmax} units box region 2 block -0.001 1.95383522434029 -0.001 1.12804729272504 27.6304027290431 28.5514494866779 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 32*${layer_z}-0.001 variable zmax equal 32*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 3 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 3 block -0.001 1.95383522434029 -0.001 1.12804729272504 28.5514494866779 ${zmax} units box region 3 block -0.001 1.95383522434029 -0.001 1.12804729272504 28.5514494866779 29.4724962443126 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 33*${layer_z}-0.001 variable zmax equal 33*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 4 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 4 block -0.001 1.95383522434029 -0.001 1.12804729272504 29.4724962443126 ${zmax} units box region 4 block -0.001 1.95383522434029 -0.001 1.12804729272504 29.4724962443126 30.3935430019474 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 34*${layer_z}-0.001 variable zmax equal 34*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 5 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 5 block -0.001 1.95383522434029 -0.001 1.12804729272504 30.3935430019474 ${zmax} units box region 5 block -0.001 1.95383522434029 -0.001 1.12804729272504 30.3935430019474 31.3145897595822 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 35*${layer_z}-0.001 variable zmax equal 35*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 6 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 6 block -0.001 1.95383522434029 -0.001 1.12804729272504 31.3145897595822 ${zmax} units box region 6 block -0.001 1.95383522434029 -0.001 1.12804729272504 31.3145897595822 32.235636517217 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 36*${layer_z}-0.001 variable zmax equal 36*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 7 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 7 block -0.001 1.95383522434029 -0.001 1.12804729272504 32.235636517217 ${zmax} units box region 7 block -0.001 1.95383522434029 -0.001 1.12804729272504 32.235636517217 33.1566832748517 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 37*${layer_z}-0.001 variable zmax equal 37*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 8 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 8 block -0.001 1.95383522434029 -0.001 1.12804729272504 33.1566832748517 ${zmax} units box region 8 block -0.001 1.95383522434029 -0.001 1.12804729272504 33.1566832748517 34.0777300324865 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 38*${layer_z}-0.001 variable zmax equal 38*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 9 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 9 block -0.001 1.95383522434029 -0.001 1.12804729272504 34.0777300324865 ${zmax} units box region 9 block -0.001 1.95383522434029 -0.001 1.12804729272504 34.0777300324865 34.9987767901213 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 39*${layer_z}-0.001 variable zmax equal 39*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 10 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 10 block -0.001 1.95383522434029 -0.001 1.12804729272504 34.9987767901213 ${zmax} units box region 10 block -0.001 1.95383522434029 -0.001 1.12804729272504 34.9987767901213 35.919823547756 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 40*${layer_z}-0.001 variable zmax equal 40*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 11 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 11 block -0.001 1.95383522434029 -0.001 1.12804729272504 35.919823547756 ${zmax} units box region 11 block -0.001 1.95383522434029 -0.001 1.12804729272504 35.919823547756 36.8408703053908 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 41*${layer_z}-0.001 variable zmax equal 41*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 12 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 12 block -0.001 1.95383522434029 -0.001 1.12804729272504 36.8408703053908 ${zmax} units box region 12 block -0.001 1.95383522434029 -0.001 1.12804729272504 36.8408703053908 37.7619170630256 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 42*${layer_z}-0.001 variable zmax equal 42*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 13 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 13 block -0.001 1.95383522434029 -0.001 1.12804729272504 37.7619170630256 ${zmax} units box region 13 block -0.001 1.95383522434029 -0.001 1.12804729272504 37.7619170630256 38.6829638206603 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 43*${layer_z}-0.001 variable zmax equal 43*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 14 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 14 block -0.001 1.95383522434029 -0.001 1.12804729272504 38.6829638206603 ${zmax} units box region 14 block -0.001 1.95383522434029 -0.001 1.12804729272504 38.6829638206603 39.6040105782951 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 44*${layer_z}-0.001 variable zmax equal 44*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 15 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 15 block -0.001 1.95383522434029 -0.001 1.12804729272504 39.6040105782951 ${zmax} units box region 15 block -0.001 1.95383522434029 -0.001 1.12804729272504 39.6040105782951 40.5250573359299 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 45*${layer_z}-0.001 variable zmax equal 45*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 16 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 16 block -0.001 1.95383522434029 -0.001 1.12804729272504 40.5250573359299 ${zmax} units box region 16 block -0.001 1.95383522434029 -0.001 1.12804729272504 40.5250573359299 41.4461040935646 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 46*${layer_z}-0.001 variable zmax equal 46*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 17 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 17 block -0.001 1.95383522434029 -0.001 1.12804729272504 41.4461040935646 ${zmax} units box region 17 block -0.001 1.95383522434029 -0.001 1.12804729272504 41.4461040935646 42.3671508511994 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 47*${layer_z}-0.001 variable zmax equal 47*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 18 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 18 block -0.001 1.95383522434029 -0.001 1.12804729272504 42.3671508511994 ${zmax} units box region 18 block -0.001 1.95383522434029 -0.001 1.12804729272504 42.3671508511994 43.2881976088342 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 48*${layer_z}-0.001 variable zmax equal 48*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 19 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 19 block -0.001 1.95383522434029 -0.001 1.12804729272504 43.2881976088342 ${zmax} units box region 19 block -0.001 1.95383522434029 -0.001 1.12804729272504 43.2881976088342 44.209244366469 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 49*${layer_z}-0.001 variable zmax equal 49*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 20 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 20 block -0.001 1.95383522434029 -0.001 1.12804729272504 44.209244366469 ${zmax} units box region 20 block -0.001 1.95383522434029 -0.001 1.12804729272504 44.209244366469 45.1302911241037 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 50*${layer_z}-0.001 variable zmax equal 50*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 21 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 21 block -0.001 1.95383522434029 -0.001 1.12804729272504 45.1302911241037 ${zmax} units box region 21 block -0.001 1.95383522434029 -0.001 1.12804729272504 45.1302911241037 46.0513378817385 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 51*${layer_z}-0.001 variable zmax equal 51*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 22 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 22 block -0.001 1.95383522434029 -0.001 1.12804729272504 46.0513378817385 ${zmax} units box region 22 block -0.001 1.95383522434029 -0.001 1.12804729272504 46.0513378817385 46.9723846393733 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 52*${layer_z}-0.001 variable zmax equal 52*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 23 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 23 block -0.001 1.95383522434029 -0.001 1.12804729272504 46.9723846393733 ${zmax} units box region 23 block -0.001 1.95383522434029 -0.001 1.12804729272504 46.9723846393733 47.893431397008 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 53*${layer_z}-0.001 variable zmax equal 53*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 24 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 24 block -0.001 1.95383522434029 -0.001 1.12804729272504 47.893431397008 ${zmax} units box region 24 block -0.001 1.95383522434029 -0.001 1.12804729272504 47.893431397008 48.8144781546428 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 54*${layer_z}-0.001 variable zmax equal 54*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 25 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 25 block -0.001 1.95383522434029 -0.001 1.12804729272504 48.8144781546428 ${zmax} units box region 25 block -0.001 1.95383522434029 -0.001 1.12804729272504 48.8144781546428 49.7355249122776 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 55*${layer_z}-0.001 variable zmax equal 55*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 26 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 26 block -0.001 1.95383522434029 -0.001 1.12804729272504 49.7355249122776 ${zmax} units box region 26 block -0.001 1.95383522434029 -0.001 1.12804729272504 49.7355249122776 50.6565716699124 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 56*${layer_z}-0.001 variable zmax equal 56*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 27 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 27 block -0.001 1.95383522434029 -0.001 1.12804729272504 50.6565716699124 ${zmax} units box region 27 block -0.001 1.95383522434029 -0.001 1.12804729272504 50.6565716699124 51.5776184275471 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 57*${layer_z}-0.001 variable zmax equal 57*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 28 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 28 block -0.001 1.95383522434029 -0.001 1.12804729272504 51.5776184275471 ${zmax} units box region 28 block -0.001 1.95383522434029 -0.001 1.12804729272504 51.5776184275471 52.4986651851819 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)*0.92104675763477-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 58*${layer_z}-0.001 variable zmax equal 58*0.92104675763477-0.001 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 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region 29 block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region 29 block -0.001 1.95383522434029 -0.001 1.12804729272504 52.4986651851819 ${zmax} units box region 29 block -0.001 1.95383522434029 -0.001 1.12804729272504 52.4986651851819 53.4197119428167 units box next i jump SELF start_of_loop_region variable i delete variable j delete # Declare group for the rigid blocks for intrinsic stacking fault variable zmin equal (15-1.0)*${layer_z}-0.001 variable zmin equal (15-1.0)*0.92104675763477-0.001 variable zmax equal (45-1.0)*${layer_z}+0.001 variable zmax equal (45-1.0)*0.92104675763477+0.001 region stack_region block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region stack_region block -0.001 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region stack_region block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region stack_region block -0.001 1.95383522434029 -0.001 1.12804729272504 12.8936546068868 ${zmax} units box region stack_region block -0.001 1.95383522434029 -0.001 1.12804729272504 12.8936546068868 40.5270573359299 units box # Declare group for the rigid blocks for the extrisic stacking fault variable zmin equal (16-1.0)*${layer_z}-0.001 variable zmin equal (16-1.0)*0.92104675763477-0.001 variable zmax equal (44-1.0)*${layer_z}+0.001 variable zmax equal (44-1.0)*0.92104675763477+0.001 region twin_region block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region twin_region block -0.001 1.95383522434029 -0.001 ${ydim} ${zmin} ${zmax} units box region twin_region block -0.001 1.95383522434029 -0.001 1.12804729272504 ${zmin} ${zmax} units box region twin_region block -0.001 1.95383522434029 -0.001 1.12804729272504 13.8147013645216 ${zmax} units box region twin_region block -0.001 1.95383522434029 -0.001 1.12804729272504 13.8147013645216 39.6060105782951 units box # Create simulation box and atoms region whole block 0-0.001 ${xdim}+0.01 0-0.01 ${ydim}+0.01 0-0.01 ${zdim}+0.01 units box region whole block 0-0.001 1.95383522434029+0.01 0-0.01 ${ydim}+0.01 0-0.01 ${zdim}+0.01 units box region whole block 0-0.001 1.95383522434029+0.01 0-0.01 1.12804729272504+0.01 0-0.01 ${zdim}+0.01 units box region whole block 0-0.001 1.95383522434029+0.01 0-0.01 1.12804729272504+0.01 0-0.01 53.4207119428167+0.01 units box create_box 1 whole Created orthogonal box = (0 0 0) to (1.95384 1.12805 53.4207) 1 by 1 by 1 MPI processor grid lattice fcc ${latparam} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 lattice fcc 1.59529978037 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 Lattice spacing in x,y,z = 2.60511 2.25609 2.76314 create_atoms 1 region whole Created 116 atoms Time spent = 0.00104403 secs # Define the interatomic potentials pair_style kim LJ_ElliottAkerson_2015_Universal__MO_959249795837_003 pair_coeff * * Ne 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 # Compute initial energy and output compute peratom all pe/atom compute eatoms all reduce sum c_peratom thermo 100 thermo_style custom step pe c_eatoms press pxx pyy pzz pe temp #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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.2653, bins = 1 1 6 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:933) 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