LAMMPS (11 Aug 2017) clear units metal dimension 3 boundary p p p atom_style atomic lattice fcc 4.0501806736 Lattice spacing in x,y,z = 4.05018 4.05018 4.05018 region whole block 0 71.6550107947471 -71.6590609754207 71.6590609754207 0 4.0501806736 units box create_box 2 whole Created orthogonal box = (0 -71.6591 0) to (71.655 71.6591 4.05018) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 71.6590609754207 INF INF units box lattice fcc 4.0501806736 orient x 13 -12 0 orient y 12 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.72324 5.72324 4.05018 create_atoms 1 region upper Created 1254 atoms group upper type 1 1254 atoms in group upper mass 1 26.981538 displace_atoms upper move 7.96131270582936 0 0.3333333333333333 region lower block INF INF -71.6590609754207 0.0 INF INF units box lattice fcc 4.0501806736 orient x 13 12 0 orient y -12 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.72324 5.72324 4.05018 create_atoms 2 region lower Created 1254 atoms group lower type 2 1254 atoms in group lower displace_atoms lower move -7.96131270582936 0 -0.3333333333333333 mass 2 26.981538 pair_style kim LAMMPSvirial EAM_Dynamo_Zhou_Johnson_Al__MO_131650261510_004 pair_coeff * * Al Al neighbor 2.0 bin neigh_modify delay 10 check yes delete_atoms overlap 2.0250903368 all all Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.40393 ghost atom cutoff = 8.40393 binsize = 4.20196, bins = 18 35 1 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: half, newton off pair build: half/bin/newtoff stencil: half/bin/3d/newtoff bin: standard Deleted 32 atoms, new total = 2476 min_style cg minimize 1e-15 1e-15 5000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../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 = 8.40393 ghost atom cutoff = 8.40393 binsize = 4.20196, bins = 18 35 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: half, newton off pair build: half/bin/newtoff stencil: half/bin/3d/newtoff bin: standard Per MPI rank memory allocation (min/avg/max) = 9.518 | 9.518 | 9.518 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8833.2453 0 -8833.2453 -1771.3582 151 0 -8858.254 0 -8858.254 -5593.4944 Loop time of 3.39238 on 1 procs for 151 steps with 2476 atoms 64.3% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -8833.2452572 -8858.25402819 -8858.25402819 Force two-norm initial, final = 12.8375 0.00920646 Force max component initial, final = 1.98865 0.00174081 Final line search alpha, max atom move = 0.00012207 2.12501e-07 Iterations, force evaluations = 151 304 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2834 | 3.2834 | 3.2834 | 0.0 | 96.79 Neigh | 0.060763 | 0.060763 | 0.060763 | 0.0 | 1.79 Comm | 0.019247 | 0.019247 | 0.019247 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02901 | | | 0.86 Nlocal: 2476 ave 2476 max 2476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14564 ave 14564 max 14564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 291466 ave 291466 max 291466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 291466 Ave neighs/atom = 117.716 Neighbor list builds = 4 Dangerous builds = 0 fix 1 all box/relax x 0.0 z 0.0 couple none vmax 0.001 minimize 1.0e-25 1.0e-25 1000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168) Per MPI rank memory allocation (min/avg/max) = 9.518 | 9.518 | 9.518 Mbytes Step Temp E_pair E_mol TotEng Press Volume 151 0 -8858.254 0 -8858.254 -5593.4944 41593.175 158 0 -8858.6496 0 -8858.6496 -1223.343 41354.672 Loop time of 0.331172 on 1 procs for 7 steps with 2476 atoms 95.4% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -8858.25402819 -8858.64956445 -8858.64956445 Force two-norm initial, final = 180.969 0.158732 Force max component initial, final = 136.546 0.139365 Final line search alpha, max atom move = 3.0483e-07 4.24824e-08 Iterations, force evaluations = 7 42 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31986 | 0.31986 | 0.31986 | 0.0 | 96.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0021904 | 0.0021904 | 0.0021904 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009124 | | | 2.75 Nlocal: 2476 ave 2476 max 2476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14574 ave 14574 max 14574 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 291567 ave 291567 max 291567 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 291567 Ave neighs/atom = 117.757 Neighbor list builds = 0 Dangerous builds = 0 unfix 1 compute csym all centro/atom fcc compute csymsum all reduce sum c_csym compute eng all pe/atom compute eatoms all reduce sum c_eng compute distance all pair/local dist compute mindist all reduce min c_distance reset_timestep 0 run 0 WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.40393 ghost atom cutoff = 8.40393 binsize = 4.20196, bins = 18 35 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: half, newton off pair build: half/bin/newtoff stencil: half/bin/3d/newtoff bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 9.031 | 9.031 | 9.031 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8858.6496 0 -8858.6496 -1223.343 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2476 atoms 0.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 2476 ave 2476 max 2476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14574 ave 14574 max 14574 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 291619 ave 291619 max 291619 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 291619 Ave neighs/atom = 117.778 Neighbor list builds = 0 Dangerous builds = 0 thermo 0 thermo_style custom step pe lx ly lz press pxx pyy pzz c_eatoms c_mindist c_csymsum run 0 WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) Per MPI rank memory allocation (min/avg/max) = 9.031 | 9.031 | 9.031 Mbytes Step PotEng Lx Ly Lz Press Pxx Pyy Pzz c_eatoms c_mindist c_csymsum 0 -8858.6496 71.516469 143.31812 4.0347572 -1223.343 0.86903403 -3676.2769 5.378745 -8858.6496 2.6081211 189.72991 Loop time of 0 on 1 procs for 0 steps with 2476 atoms 0.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0 | | | 0.00 Nlocal: 2476 ave 2476 max 2476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14574 ave 14574 max 14574 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 291619 ave 291619 max 291619 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 346816 ave 346816 max 346816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 346816 Ave neighs/atom = 140.071 Neighbor list builds = 0 Dangerous builds = 0 variable total_energy equal c_eatoms print "${total_energy}" file output/dump_085.4188/energy.out -8858.6495644493 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_085.4188/numatoms.out 2476 variable minimum_distance equal c_mindist print "${minimum_distance}" file output/dump_085.4188/mindistance.out 2.60812114366754 write_dump all cfg output/dump_085.4188/dump_post.cfg mass type xs ys zs id type xs ys zs c_csym c_eng modify element Al Al print "This indicates that LAMMPS ran successfully" file output/dump_085.4188/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:03