LAMMPS (11 Aug 2017) clear units metal dimension 3 boundary p p p atom_style atomic lattice fcc 4.04525975883 Lattice spacing in x,y,z = 4.04526 4.04526 4.04526 region whole block 0 44.68135444457724 -44.68539970433607 44.68539970433607 0 4.045259758830001 units box create_box 2 whole Created orthogonal box = (0 -44.6854 0) to (44.6814 44.6854 4.04526) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 44.68539970433607 INF INF units box lattice fcc 4.04525975883 orient x 11 -1 0 orient y 1 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.39489 4.39489 4.04526 create_atoms 1 region upper Created 489 atoms group upper type 1 489 atoms in group upper mass 1 26.981538 displace_atoms upper move 4.970412457734268 0 0.3333333333333333 region lower block INF INF -44.68539970433607 0.0 INF INF units box lattice fcc 4.04525975883 orient x 11 1 0 orient y -1 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.39489 4.39489 4.04526 create_atoms 2 region lower Created 489 atoms group lower type 2 489 atoms in group lower displace_atoms lower move -4.970412457734268 0 -0.3333333333333333 mass 2 26.981538 pair_style kim LAMMPSvirial EAM_Dynamo_Mendelev_Kramer_Al__MO_106969701023_004 pair_coeff * * Al Al neighbor 2.0 bin neigh_modify delay 10 check yes delete_atoms overlap 2.02262987942 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 11 22 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 17 atoms, new total = 961 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 11 22 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) = 4.94 | 4.94 | 4.94 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3255.9624 0 -3255.9624 -1162.4493 248 0 -3267.2302 0 -3267.2302 -6435.9024 Loop time of 1.87624 on 1 procs for 248 steps with 961 atoms 79.5% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3255.9623635 -3267.23024897 -3267.23024897 Force two-norm initial, final = 16.2678 1.87787e-06 Force max component initial, final = 5.49593 3.5011e-07 Final line search alpha, max atom move = 1 3.5011e-07 Iterations, force evaluations = 248 486 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8519 | 1.8519 | 1.8519 | 0.0 | 98.70 Neigh | 0.003361 | 0.003361 | 0.003361 | 0.0 | 0.18 Comm | 0.011355 | 0.011355 | 0.011355 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009657 | | | 0.51 Nlocal: 961 ave 961 max 961 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6934 ave 6934 max 6934 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 115830 ave 115830 max 115830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 115830 Ave neighs/atom = 120.531 Neighbor list builds = 1 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) = 4.941 | 4.941 | 4.941 Mbytes Step Temp E_pair E_mol TotEng Press Volume 248 0 -3267.2302 0 -3267.2302 -6435.9024 16153.565 1248 0 -3267.4614 0 -3267.4614 -1230.0796 16049.364 Loop time of 7.33836 on 1 procs for 1000 steps with 961 atoms 90.3% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -3267.23024897 -3267.46141131 -3267.46141131 Force two-norm initial, final = 85.2326 0.00314496 Force max component initial, final = 72.7965 0.00159171 Final line search alpha, max atom move = 0.452848 0.000720804 Iterations, force evaluations = 1000 1994 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.0433 | 7.0433 | 7.0433 | 0.0 | 95.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.050974 | 0.050974 | 0.050974 | 0.0 | 0.69 Output | 1.1921e-05 | 1.1921e-05 | 1.1921e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2441 | | | 3.33 Nlocal: 961 ave 961 max 961 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6939 ave 6939 max 6939 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 115855 ave 115855 max 115855 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 115855 Ave neighs/atom = 120.557 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 11 22 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) = 5.079 | 5.079 | 5.079 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3267.4614 0 -3267.4614 -1230.0796 Loop time of 9.53674e-07 on 1 procs for 0 steps with 961 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: 961 ave 961 max 961 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6939 ave 6939 max 6939 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 116212 ave 116212 max 116212 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 = 116212 Ave neighs/atom = 120.928 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) = 5.079 | 5.079 | 5.079 Mbytes Step PotEng Lx Ly Lz Press Pxx Pyy Pzz c_eatoms c_mindist c_csymsum 0 -3267.4614 44.654369 89.370799 4.0215941 -1230.0796 0.047317599 -3690.4442 0.15796802 -3267.4614 2.5321176 377.03629 Loop time of 1.19209e-06 on 1 procs for 0 steps with 961 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 | | 1.192e-06 | | |100.00 Nlocal: 961 ave 961 max 961 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6939 ave 6939 max 6939 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 116212 ave 116212 max 116212 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 137070 ave 137070 max 137070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137070 Ave neighs/atom = 142.633 Neighbor list builds = 0 Dangerous builds = 0 variable total_energy equal c_eatoms print "${total_energy}" file output/dump_010.3889/energy.out -3267.46141131071 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_010.3889/numatoms.out 961 variable minimum_distance equal c_mindist print "${minimum_distance}" file output/dump_010.3889/mindistance.out 2.53211758053211 write_dump all cfg output/dump_010.3889/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_010.3889/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:09