LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) 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 ${neigh_skin} bin neighbor 2 bin # Atom definition variable latparam_converted equal 2.5751821175217633*${_u_distance} variable latparam_converted equal 2.5751821175217633*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 (2.5751821175217633*sqrt(6)/2)*${nlat_x} variable xdim equal (2.5751821175217633*sqrt(6)/2)*1 variable ydim equal (2.5751821175217633*sqrt(2)/2)*${nlat_y} variable ydim equal (2.5751821175217633*sqrt(2)/2)*1 # Area of the stacking fault plane in Angstrom^2 variable Area equal 2*${xdim}*${ydim} variable Area equal 2*3.15394109133411*${ydim} variable Area equal 2*3.15394109133411*1.82092873808997 # Now convert xdim and ydim to the active unit set and do z direction variable xdim equal ${xdim}*${_u_distance} variable xdim equal 3.15394109133411*${_u_distance} variable xdim equal 3.15394109133411*1 variable ydim equal ${ydim}*${_u_distance} variable ydim equal 1.82092873808997*${_u_distance} variable ydim equal 1.82092873808997*1 variable zdim equal (${latparam_converted}/sqrt(3))*${nlat_z} variable zdim equal (2.57518211752176/sqrt(3))*${nlat_z} variable zdim equal (2.57518211752176/sqrt(3))*58 variable layer_z equal (${latparam_converted}/sqrt(3)) variable layer_z equal (2.57518211752176/sqrt(3)) # Geometry definition lattice fcc ${latparam_converted} lattice fcc 2.57518211752176 Lattice spacing in x,y,z = 2.57518 2.57518 2.57518 # 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 30*${layer_z}-0.001 variable zmax equal 30*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 1 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 1 block -0.001 3.15394109133411 -0.001 1.82092873808997 43.1156805741415 ${zmax} units box region 1 block -0.001 3.15394109133411 -0.001 1.82092873808997 43.1156805741415 44.602462662905 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 31*${layer_z}-0.001 variable zmax equal 31*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 2 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 2 block -0.001 3.15394109133411 -0.001 1.82092873808997 44.602462662905 ${zmax} units box region 2 block -0.001 3.15394109133411 -0.001 1.82092873808997 44.602462662905 46.0892447516685 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 32*${layer_z}-0.001 variable zmax equal 32*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 3 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 3 block -0.001 3.15394109133411 -0.001 1.82092873808997 46.0892447516685 ${zmax} units box region 3 block -0.001 3.15394109133411 -0.001 1.82092873808997 46.0892447516685 47.576026840432 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 33*${layer_z}-0.001 variable zmax equal 33*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 4 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 4 block -0.001 3.15394109133411 -0.001 1.82092873808997 47.576026840432 ${zmax} units box region 4 block -0.001 3.15394109133411 -0.001 1.82092873808997 47.576026840432 49.0628089291955 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 34*${layer_z}-0.001 variable zmax equal 34*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 5 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 5 block -0.001 3.15394109133411 -0.001 1.82092873808997 49.0628089291955 ${zmax} units box region 5 block -0.001 3.15394109133411 -0.001 1.82092873808997 49.0628089291955 50.549591017959 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 35*${layer_z}-0.001 variable zmax equal 35*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 6 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 6 block -0.001 3.15394109133411 -0.001 1.82092873808997 50.549591017959 ${zmax} units box region 6 block -0.001 3.15394109133411 -0.001 1.82092873808997 50.549591017959 52.0363731067225 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 36*${layer_z}-0.001 variable zmax equal 36*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 7 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 7 block -0.001 3.15394109133411 -0.001 1.82092873808997 52.0363731067225 ${zmax} units box region 7 block -0.001 3.15394109133411 -0.001 1.82092873808997 52.0363731067225 53.523155195486 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 37*${layer_z}-0.001 variable zmax equal 37*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 8 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 8 block -0.001 3.15394109133411 -0.001 1.82092873808997 53.523155195486 ${zmax} units box region 8 block -0.001 3.15394109133411 -0.001 1.82092873808997 53.523155195486 55.0099372842495 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 38*${layer_z}-0.001 variable zmax equal 38*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 9 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 9 block -0.001 3.15394109133411 -0.001 1.82092873808997 55.0099372842495 ${zmax} units box region 9 block -0.001 3.15394109133411 -0.001 1.82092873808997 55.0099372842495 56.496719373013 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 39*${layer_z}-0.001 variable zmax equal 39*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 10 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 10 block -0.001 3.15394109133411 -0.001 1.82092873808997 56.496719373013 ${zmax} units box region 10 block -0.001 3.15394109133411 -0.001 1.82092873808997 56.496719373013 57.9835014617765 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 40*${layer_z}-0.001 variable zmax equal 40*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 11 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 11 block -0.001 3.15394109133411 -0.001 1.82092873808997 57.9835014617765 ${zmax} units box region 11 block -0.001 3.15394109133411 -0.001 1.82092873808997 57.9835014617765 59.47028355054 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 41*${layer_z}-0.001 variable zmax equal 41*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 12 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 12 block -0.001 3.15394109133411 -0.001 1.82092873808997 59.47028355054 ${zmax} units box region 12 block -0.001 3.15394109133411 -0.001 1.82092873808997 59.47028355054 60.9570656393035 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 42*${layer_z}-0.001 variable zmax equal 42*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 13 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 13 block -0.001 3.15394109133411 -0.001 1.82092873808997 60.9570656393035 ${zmax} units box region 13 block -0.001 3.15394109133411 -0.001 1.82092873808997 60.9570656393035 62.443847728067 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 43*${layer_z}-0.001 variable zmax equal 43*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 14 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 14 block -0.001 3.15394109133411 -0.001 1.82092873808997 62.443847728067 ${zmax} units box region 14 block -0.001 3.15394109133411 -0.001 1.82092873808997 62.443847728067 63.9306298168305 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 44*${layer_z}-0.001 variable zmax equal 44*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 15 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 15 block -0.001 3.15394109133411 -0.001 1.82092873808997 63.9306298168305 ${zmax} units box region 15 block -0.001 3.15394109133411 -0.001 1.82092873808997 63.9306298168305 65.417411905594 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 45*${layer_z}-0.001 variable zmax equal 45*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 16 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 16 block -0.001 3.15394109133411 -0.001 1.82092873808997 65.417411905594 ${zmax} units box region 16 block -0.001 3.15394109133411 -0.001 1.82092873808997 65.417411905594 66.9041939943575 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 46*${layer_z}-0.001 variable zmax equal 46*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 17 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 17 block -0.001 3.15394109133411 -0.001 1.82092873808997 66.9041939943575 ${zmax} units box region 17 block -0.001 3.15394109133411 -0.001 1.82092873808997 66.9041939943575 68.390976083121 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 47*${layer_z}-0.001 variable zmax equal 47*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 18 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 18 block -0.001 3.15394109133411 -0.001 1.82092873808997 68.390976083121 ${zmax} units box region 18 block -0.001 3.15394109133411 -0.001 1.82092873808997 68.390976083121 69.8777581718845 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 48*${layer_z}-0.001 variable zmax equal 48*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 19 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 19 block -0.001 3.15394109133411 -0.001 1.82092873808997 69.8777581718845 ${zmax} units box region 19 block -0.001 3.15394109133411 -0.001 1.82092873808997 69.8777581718845 71.364540260648 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 49*${layer_z}-0.001 variable zmax equal 49*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 20 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 20 block -0.001 3.15394109133411 -0.001 1.82092873808997 71.364540260648 ${zmax} units box region 20 block -0.001 3.15394109133411 -0.001 1.82092873808997 71.364540260648 72.8513223494115 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 50*${layer_z}-0.001 variable zmax equal 50*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 21 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 21 block -0.001 3.15394109133411 -0.001 1.82092873808997 72.8513223494115 ${zmax} units box region 21 block -0.001 3.15394109133411 -0.001 1.82092873808997 72.8513223494115 74.338104438175 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 51*${layer_z}-0.001 variable zmax equal 51*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 22 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 22 block -0.001 3.15394109133411 -0.001 1.82092873808997 74.338104438175 ${zmax} units box region 22 block -0.001 3.15394109133411 -0.001 1.82092873808997 74.338104438175 75.8248865269385 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 52*${layer_z}-0.001 variable zmax equal 52*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 23 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 23 block -0.001 3.15394109133411 -0.001 1.82092873808997 75.8248865269385 ${zmax} units box region 23 block -0.001 3.15394109133411 -0.001 1.82092873808997 75.8248865269385 77.311668615702 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 53*${layer_z}-0.001 variable zmax equal 53*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 24 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 24 block -0.001 3.15394109133411 -0.001 1.82092873808997 77.311668615702 ${zmax} units box region 24 block -0.001 3.15394109133411 -0.001 1.82092873808997 77.311668615702 78.7984507044655 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 54*${layer_z}-0.001 variable zmax equal 54*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 25 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 25 block -0.001 3.15394109133411 -0.001 1.82092873808997 78.7984507044655 ${zmax} units box region 25 block -0.001 3.15394109133411 -0.001 1.82092873808997 78.7984507044655 80.285232793229 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 55*${layer_z}-0.001 variable zmax equal 55*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 26 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 26 block -0.001 3.15394109133411 -0.001 1.82092873808997 80.285232793229 ${zmax} units box region 26 block -0.001 3.15394109133411 -0.001 1.82092873808997 80.285232793229 81.7720148819925 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 56*${layer_z}-0.001 variable zmax equal 56*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 27 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 27 block -0.001 3.15394109133411 -0.001 1.82092873808997 81.7720148819925 ${zmax} units box region 27 block -0.001 3.15394109133411 -0.001 1.82092873808997 81.7720148819925 83.258796970756 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 57*${layer_z}-0.001 variable zmax equal 57*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 28 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 28 block -0.001 3.15394109133411 -0.001 1.82092873808997 83.258796970756 ${zmax} units box region 28 block -0.001 3.15394109133411 -0.001 1.82092873808997 83.258796970756 84.7455790595195 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)*1.4867820887635-0.001 variable zmax equal ${j}*${layer_z}-0.001 variable zmax equal 58*${layer_z}-0.001 variable zmax equal 58*1.4867820887635-0.001 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 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region 29 block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region 29 block -0.001 3.15394109133411 -0.001 1.82092873808997 84.7455790595195 ${zmax} units box region 29 block -0.001 3.15394109133411 -0.001 1.82092873808997 84.7455790595195 86.232361148283 units box next i jump SELF start_of_loop_region variable i delete variable j delete # Declare group for the rigid blocks for intrinsic stacking fault variable zmin equal (15-1.0)*${layer_z}-0.001 variable zmin equal (15-1.0)*1.4867820887635-0.001 variable zmax equal (45-1.0)*${layer_z}+0.001 variable zmax equal (45-1.0)*1.4867820887635+0.001 region stack_region block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region stack_region block -0.001 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region stack_region block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region stack_region block -0.001 3.15394109133411 -0.001 1.82092873808997 20.813949242689 ${zmax} units box region stack_region block -0.001 3.15394109133411 -0.001 1.82092873808997 20.813949242689 65.419411905594 units box # Declare group for the rigid blocks for the extrisic stacking fault variable zmin equal (16-1.0)*${layer_z}-0.001 variable zmin equal (16-1.0)*1.4867820887635-0.001 variable zmax equal (44-1.0)*${layer_z}+0.001 variable zmax equal (44-1.0)*1.4867820887635+0.001 region twin_region block -0.001 ${xdim} -0.001 ${ydim} ${zmin} ${zmax} units box region twin_region block -0.001 3.15394109133411 -0.001 ${ydim} ${zmin} ${zmax} units box region twin_region block -0.001 3.15394109133411 -0.001 1.82092873808997 ${zmin} ${zmax} units box region twin_region block -0.001 3.15394109133411 -0.001 1.82092873808997 22.3007313314525 ${zmax} units box region twin_region block -0.001 3.15394109133411 -0.001 1.82092873808997 22.3007313314525 63.9326298168305 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 3.15394109133411+0.001 0-0.001 ${ydim}+0.001 0-0.001 ${zdim}+0.001 units box region whole block 0-0.001 3.15394109133411+0.001 0-0.001 1.82092873808997+0.001 0-0.001 ${zdim}+0.001 units box region whole block 0-0.001 3.15394109133411+0.001 0-0.001 1.82092873808997+0.001 0-0.001 86.2333611482829+0.001 units box create_box 1 whole Created orthogonal box = (0 0 0) to (3.15394 1.82093 86.2334) 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 2.57518211752176 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 Lattice spacing in x,y,z = 4.20525 3.64186 4.46035 create_atoms 1 region whole Created 116 atoms create_atoms CPU = 0.00105786 secs # Define the interatomic potentials pair_style kim SNAP_ZuoChenLi_2019quadratic_Ni__MO_263593395744_000 pair_coeff * * Ni 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 2 1 30 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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:931) Per MPI rank memory allocation (min/avg/max) = 4.447 | 4.447 | 4.447 Mbytes Step v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal Temp v_temp_metal 0 -23504.49 971575.63 971575.63 1962255.1 1962255.1 -1009783.4 0 0 100 -36500.724 -1.1058972e+08 -1.1058972e+08 -1.1871079e+08 -1.1871099e+08 -94347383 0 0 ERROR on proc 0: Neighbor list overflow, boost neigh_modify one (src/npair_full_bin_atomonly.cpp:88) Last command: minimize 1e-25 1e-25 10000 10000