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 3.74070501328 # 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 (3.74070501328*sqrt(6)/2)*\${nlat_x} variable xdim equal (3.74070501328*sqrt(6)/2)*1 variable ydim equal (\${latparam}*sqrt(2)/2)*\${nlat_y} variable ydim equal (3.74070501328*sqrt(2)/2)*\${nlat_y} variable ydim equal (3.74070501328*sqrt(2)/2)*1 variable zdim equal (\${latparam}/sqrt(3))*\${nlat_z} variable zdim equal (3.74070501328/sqrt(3))*\${nlat_z} variable zdim equal (3.74070501328/sqrt(3))*58 variable layer_z equal (\${latparam}/sqrt(3)) variable layer_z equal (3.74070501328/sqrt(3)) # Area of the stacking fault plane in Angstrom^2 variable Area equal 2*\${xdim}*\${ydim} variable Area equal 2*4.58140928040349*\${ydim} variable Area equal 2*4.58140928040349*2.6450778813088 # Geometry definition lattice fcc \${latparam} lattice fcc 3.74070501328 Lattice spacing in x,y,z = 3.74071 3.74071 3.74071 # 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 30*\${layer_z}-0.001 variable zmax equal 30*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 1 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 1 block -0.001 4.58140928040349 -0.001 2.6450778813088 62.6302143449095 \${zmax} units box region 1 block -0.001 4.58140928040349 -0.001 2.6450778813088 62.6302143449095 64.7899113912857 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 31*\${layer_z}-0.001 variable zmax equal 31*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 2 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 2 block -0.001 4.58140928040349 -0.001 2.6450778813088 64.7899113912857 \${zmax} units box region 2 block -0.001 4.58140928040349 -0.001 2.6450778813088 64.7899113912857 66.9496084376619 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 32*\${layer_z}-0.001 variable zmax equal 32*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 3 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 3 block -0.001 4.58140928040349 -0.001 2.6450778813088 66.9496084376619 \${zmax} units box region 3 block -0.001 4.58140928040349 -0.001 2.6450778813088 66.9496084376619 69.1093054840381 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 33*\${layer_z}-0.001 variable zmax equal 33*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 4 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 4 block -0.001 4.58140928040349 -0.001 2.6450778813088 69.1093054840381 \${zmax} units box region 4 block -0.001 4.58140928040349 -0.001 2.6450778813088 69.1093054840381 71.2690025304143 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 34*\${layer_z}-0.001 variable zmax equal 34*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 5 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 5 block -0.001 4.58140928040349 -0.001 2.6450778813088 71.2690025304143 \${zmax} units box region 5 block -0.001 4.58140928040349 -0.001 2.6450778813088 71.2690025304143 73.4286995767905 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 35*\${layer_z}-0.001 variable zmax equal 35*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 6 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 6 block -0.001 4.58140928040349 -0.001 2.6450778813088 73.4286995767905 \${zmax} units box region 6 block -0.001 4.58140928040349 -0.001 2.6450778813088 73.4286995767905 75.5883966231666 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 36*\${layer_z}-0.001 variable zmax equal 36*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 7 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 7 block -0.001 4.58140928040349 -0.001 2.6450778813088 75.5883966231666 \${zmax} units box region 7 block -0.001 4.58140928040349 -0.001 2.6450778813088 75.5883966231666 77.7480936695428 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 37*\${layer_z}-0.001 variable zmax equal 37*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 8 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 8 block -0.001 4.58140928040349 -0.001 2.6450778813088 77.7480936695428 \${zmax} units box region 8 block -0.001 4.58140928040349 -0.001 2.6450778813088 77.7480936695428 79.907790715919 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 38*\${layer_z}-0.001 variable zmax equal 38*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 9 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 9 block -0.001 4.58140928040349 -0.001 2.6450778813088 79.907790715919 \${zmax} units box region 9 block -0.001 4.58140928040349 -0.001 2.6450778813088 79.907790715919 82.0674877622952 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 39*\${layer_z}-0.001 variable zmax equal 39*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 10 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 10 block -0.001 4.58140928040349 -0.001 2.6450778813088 82.0674877622952 \${zmax} units box region 10 block -0.001 4.58140928040349 -0.001 2.6450778813088 82.0674877622952 84.2271848086714 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 40*\${layer_z}-0.001 variable zmax equal 40*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 11 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 11 block -0.001 4.58140928040349 -0.001 2.6450778813088 84.2271848086714 \${zmax} units box region 11 block -0.001 4.58140928040349 -0.001 2.6450778813088 84.2271848086714 86.3868818550476 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 41*\${layer_z}-0.001 variable zmax equal 41*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 12 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 12 block -0.001 4.58140928040349 -0.001 2.6450778813088 86.3868818550476 \${zmax} units box region 12 block -0.001 4.58140928040349 -0.001 2.6450778813088 86.3868818550476 88.5465789014238 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 42*\${layer_z}-0.001 variable zmax equal 42*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 13 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 13 block -0.001 4.58140928040349 -0.001 2.6450778813088 88.5465789014238 \${zmax} units box region 13 block -0.001 4.58140928040349 -0.001 2.6450778813088 88.5465789014238 90.7062759478 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 43*\${layer_z}-0.001 variable zmax equal 43*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 14 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 14 block -0.001 4.58140928040349 -0.001 2.6450778813088 90.7062759478 \${zmax} units box region 14 block -0.001 4.58140928040349 -0.001 2.6450778813088 90.7062759478 92.8659729941762 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 44*\${layer_z}-0.001 variable zmax equal 44*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 15 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 15 block -0.001 4.58140928040349 -0.001 2.6450778813088 92.8659729941762 \${zmax} units box region 15 block -0.001 4.58140928040349 -0.001 2.6450778813088 92.8659729941762 95.0256700405524 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 45*\${layer_z}-0.001 variable zmax equal 45*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 16 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 16 block -0.001 4.58140928040349 -0.001 2.6450778813088 95.0256700405524 \${zmax} units box region 16 block -0.001 4.58140928040349 -0.001 2.6450778813088 95.0256700405524 97.1853670869286 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 46*\${layer_z}-0.001 variable zmax equal 46*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 17 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 17 block -0.001 4.58140928040349 -0.001 2.6450778813088 97.1853670869286 \${zmax} units box region 17 block -0.001 4.58140928040349 -0.001 2.6450778813088 97.1853670869286 99.3450641333047 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 47*\${layer_z}-0.001 variable zmax equal 47*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 18 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 18 block -0.001 4.58140928040349 -0.001 2.6450778813088 99.3450641333047 \${zmax} units box region 18 block -0.001 4.58140928040349 -0.001 2.6450778813088 99.3450641333047 101.504761179681 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 48*\${layer_z}-0.001 variable zmax equal 48*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 19 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 19 block -0.001 4.58140928040349 -0.001 2.6450778813088 101.504761179681 \${zmax} units box region 19 block -0.001 4.58140928040349 -0.001 2.6450778813088 101.504761179681 103.664458226057 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 49*\${layer_z}-0.001 variable zmax equal 49*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 20 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 20 block -0.001 4.58140928040349 -0.001 2.6450778813088 103.664458226057 \${zmax} units box region 20 block -0.001 4.58140928040349 -0.001 2.6450778813088 103.664458226057 105.824155272433 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 50*\${layer_z}-0.001 variable zmax equal 50*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 21 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 21 block -0.001 4.58140928040349 -0.001 2.6450778813088 105.824155272433 \${zmax} units box region 21 block -0.001 4.58140928040349 -0.001 2.6450778813088 105.824155272433 107.983852318809 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 51*\${layer_z}-0.001 variable zmax equal 51*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 22 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 22 block -0.001 4.58140928040349 -0.001 2.6450778813088 107.983852318809 \${zmax} units box region 22 block -0.001 4.58140928040349 -0.001 2.6450778813088 107.983852318809 110.143549365186 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 52*\${layer_z}-0.001 variable zmax equal 52*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 23 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 23 block -0.001 4.58140928040349 -0.001 2.6450778813088 110.143549365186 \${zmax} units box region 23 block -0.001 4.58140928040349 -0.001 2.6450778813088 110.143549365186 112.303246411562 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 53*\${layer_z}-0.001 variable zmax equal 53*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 24 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 24 block -0.001 4.58140928040349 -0.001 2.6450778813088 112.303246411562 \${zmax} units box region 24 block -0.001 4.58140928040349 -0.001 2.6450778813088 112.303246411562 114.462943457938 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 54*\${layer_z}-0.001 variable zmax equal 54*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 25 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 25 block -0.001 4.58140928040349 -0.001 2.6450778813088 114.462943457938 \${zmax} units box region 25 block -0.001 4.58140928040349 -0.001 2.6450778813088 114.462943457938 116.622640504314 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 55*\${layer_z}-0.001 variable zmax equal 55*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 26 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 26 block -0.001 4.58140928040349 -0.001 2.6450778813088 116.622640504314 \${zmax} units box region 26 block -0.001 4.58140928040349 -0.001 2.6450778813088 116.622640504314 118.78233755069 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 56*\${layer_z}-0.001 variable zmax equal 56*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 27 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 27 block -0.001 4.58140928040349 -0.001 2.6450778813088 118.78233755069 \${zmax} units box region 27 block -0.001 4.58140928040349 -0.001 2.6450778813088 118.78233755069 120.942034597067 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 57*\${layer_z}-0.001 variable zmax equal 57*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 28 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 28 block -0.001 4.58140928040349 -0.001 2.6450778813088 120.942034597067 \${zmax} units box region 28 block -0.001 4.58140928040349 -0.001 2.6450778813088 120.942034597067 123.101731643443 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)*2.15969704637619-0.001 variable zmax equal \${j}*\${layer_z}-0.001 variable zmax equal 58*\${layer_z}-0.001 variable zmax equal 58*2.15969704637619-0.001 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 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region 29 block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region 29 block -0.001 4.58140928040349 -0.001 2.6450778813088 123.101731643443 \${zmax} units box region 29 block -0.001 4.58140928040349 -0.001 2.6450778813088 123.101731643443 125.261428689819 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)*2.15969704637619-0.001 variable zmax equal (45-1.0)*\${layer_z}+0.001 variable zmax equal (45-1.0)*2.15969704637619+0.001 region stack_region block -0.001 \${xdim} -0.001 \${ydim} \${zmin} \${zmax} units box region stack_region block -0.001 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region stack_region block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region stack_region block -0.001 4.58140928040349 -0.001 2.6450778813088 30.2347586492667 \${zmax} units box region stack_region block -0.001 4.58140928040349 -0.001 2.6450778813088 30.2347586492667 95.0276700405524 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)*2.15969704637619-0.001 variable zmax equal (44-1.0)*\${layer_z}+0.001 variable zmax equal (44-1.0)*2.15969704637619+0.001 region twin_region block -0.001 \${xdim} -0.001 \${ydim} \${zmin} \${zmax} units box region twin_region block -0.001 4.58140928040349 -0.001 \${ydim} \${zmin} \${zmax} units box region twin_region block -0.001 4.58140928040349 -0.001 2.6450778813088 \${zmin} \${zmax} units box region twin_region block -0.001 4.58140928040349 -0.001 2.6450778813088 32.3944556956429 \${zmax} units box region twin_region block -0.001 4.58140928040349 -0.001 2.6450778813088 32.3944556956429 92.8679729941762 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 4.58140928040349+0.01 0-0.01 \${ydim}+0.01 0-0.01 \${zdim}+0.01 units box region whole block 0-0.001 4.58140928040349+0.01 0-0.01 2.6450778813088+0.01 0-0.01 \${zdim}+0.01 units box region whole block 0-0.001 4.58140928040349+0.01 0-0.01 2.6450778813088+0.01 0-0.01 125.262428689819+0.01 units box create_box 1 whole Created orthogonal box = (0 0 0) to (4.58141 2.64508 125.262) 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 3.74070501328 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 Lattice spacing in x,y,z = 6.10855 5.29016 6.47909 create_atoms 1 region whole Created 116 atoms Time spent = 0.00102997 secs # Define the interatomic potentials pair_style kim LJ_ElliottAkerson_2015_Universal__MO_959249795837_003 pair_coeff * * Pt 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 13 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 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