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 48.770633642351086 -48.77468382302469 48.77468382302469 0 4.0501806736 units box create_box 2 whole Created orthogonal box = (0 -48.7747 0) to (48.7706 48.7747 4.05018) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 48.77468382302469 INF INF units box lattice fcc 4.0501806736 orient x 12 -1 0 orient y 1 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.37254 4.37254 4.05018 create_atoms 1 region upper Created 582 atoms group upper type 1 582 atoms in group upper mass 1 26.981538 displace_atoms upper move 5.418717560456534 0 0.3333333333333333 region lower block INF INF -48.77468382302469 0.0 INF INF units box lattice fcc 4.0501806736 orient x 12 1 0 orient y -1 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.37254 4.37254 4.05018 create_atoms 2 region lower Created 582 atoms group lower type 2 582 atoms in group lower displace_atoms lower move -5.418717560456534 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 = 12 24 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 22 atoms, new total = 1142 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 = 12 24 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) = 4.982 | 4.982 | 4.982 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4071.7965 0 -4071.7965 -2152.3777 195 0 -4082.0272 0 -4082.0272 -4371.1046 Loop time of 1.31316 on 1 procs for 195 steps with 1142 atoms 99.9% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -4071.79645126 -4082.02716047 -4082.02716047 Force two-norm initial, final = 9.44675 0.00488219 Force max component initial, final = 2.77021 0.000758072 Final line search alpha, max atom move = 0.000488281 3.70152e-07 Iterations, force evaluations = 195 398 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2828 | 1.2828 | 1.2828 | 0.0 | 97.69 Neigh | 0.0090261 | 0.0090261 | 0.0090261 | 0.0 | 0.69 Comm | 0.012324 | 0.012324 | 0.012324 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009011 | | | 0.69 Nlocal: 1142 ave 1142 max 1142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7907 ave 7907 max 7907 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 135480 ave 135480 max 135480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135480 Ave neighs/atom = 118.634 Neighbor list builds = 2 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) = 4.982 | 4.982 | 4.982 Mbytes Step Temp E_pair E_mol TotEng Press Volume 195 0 -4082.0272 0 -4082.0272 -4371.1046 19268.915 199 0 -4082.1067 0 -4082.1067 -1530.4894 19195.824 Loop time of 0.125543 on 1 procs for 4 steps with 1142 atoms 102.0% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -4082.02716047 -4082.10669389 -4082.10669389 Force two-norm initial, final = 53.7405 0.0454989 Force max component initial, final = 39.2341 0.00797349 Final line search alpha, max atom move = 3.82738e-06 3.05176e-08 Iterations, force evaluations = 4 36 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12044 | 0.12044 | 0.12044 | 0.0 | 95.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00096679 | 0.00096679 | 0.00096679 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004138 | | | 3.30 Nlocal: 1142 ave 1142 max 1142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7913 ave 7913 max 7913 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 135527 ave 135527 max 135527 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135527 Ave neighs/atom = 118.675 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 = 12 24 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) = 5.12 | 5.12 | 5.12 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4082.1067 0 -4082.1067 -1530.4894 Loop time of 0 on 1 procs for 0 steps with 1142 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: 1142 ave 1142 max 1142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7921 ave 7921 max 7921 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 135695 ave 135695 max 135695 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 = 135695 Ave neighs/atom = 118.822 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) = 5.12 | 5.12 | 5.12 Mbytes Step PotEng Lx Ly Lz Press Pxx Pyy Pzz c_eatoms c_mindist c_csymsum 0 -4082.1067 48.66793 97.549368 4.0433323 -1530.4894 0.35561537 -4592.4883 0.6643811 -4082.1067 2.6259989 252.66088 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1142 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: 1142 ave 1142 max 1142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7921 ave 7921 max 7921 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 135695 ave 135695 max 135695 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 160196 ave 160196 max 160196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160196 Ave neighs/atom = 140.277 Neighbor list builds = 0 Dangerous builds = 0 variable total_energy equal c_eatoms print "${total_energy}" file output/dump_009.5273/energy.out -4082.10669388951 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_009.5273/numatoms.out 1142 variable minimum_distance equal c_mindist print "${minimum_distance}" file output/dump_009.5273/mindistance.out 2.62599889966199 write_dump all cfg output/dump_009.5273/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_009.5273/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:01