LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.6784521 3.6784521 3.6784521 Created orthogonal box = (0.0000000 -39.275121 0.0000000) to (22.675502 39.275121 6.3712660) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9672374 5.5122977 6.3712660 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -39.275121 0.0000000) to (22.675502 39.275121 6.3712660) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9672374 5.5122977 6.3712660 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -39.275121 0.0000000) to (22.675502 39.275121 6.3712660) create_atoms CPU = 0.001 seconds 458 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 8 26 3 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: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 912 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_024705128470_000#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 8 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.557 | 4.557 | 4.557 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3634.702 0 -3634.702 31029.93 233 0 -3839.8951 0 -3839.8951 -43187.336 Loop time of 1.4222 on 1 procs for 233 steps with 912 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3634.70203181809 -3839.89203441435 -3839.89511200588 Force two-norm initial, final = 216.73469 0.19228543 Force max component initial, final = 61.839672 0.048732924 Final line search alpha, max atom move = 1.0000000 0.048732924 Iterations, force evaluations = 233 449 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3523 | 1.3523 | 1.3523 | 0.0 | 95.09 Neigh | 0.035101 | 0.035101 | 0.035101 | 0.0 | 2.47 Comm | 0.015647 | 0.015647 | 0.015647 | 0.0 | 1.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01913 | | | 1.35 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3865.00 ave 3865 max 3865 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 61956.0 ave 61956 max 61956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61956 Ave neighs/atom = 67.934211 Neighbor list builds = 6 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 8 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 233 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.563 | 4.563 | 4.563 Mbytes Step Temp E_pair E_mol TotEng Press Volume 233 0 -3839.8951 0 -3839.8951 -43187.336 11348.284 256 0 -3845.9634 0 -3845.9634 544.71705 10989.031 Loop time of 0.0853664 on 1 procs for 23 steps with 912 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3839.89511200588 -3845.96254953286 -3845.96343377528 Force two-norm initial, final = 549.51480 6.9225004 Force max component initial, final = 418.96737 4.9030530 Final line search alpha, max atom move = 0.0023789947 0.011664337 Iterations, force evaluations = 23 25 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.079234 | 0.079234 | 0.079234 | 0.0 | 92.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00084019 | 0.00084019 | 0.00084019 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005292 | | | 6.20 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3871.00 ave 3871 max 3871 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 62008.0 ave 62008 max 62008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62008 Ave neighs/atom = 67.991228 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 8 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.701 | 4.701 | 4.701 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3845.9634 0 -3845.9634 544.71705 Loop time of 2.124e-06 on 1 procs for 0 steps with 912 atoms 141.2% CPU use with 1 MPI tasks x 1 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 | | 2.124e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3916.00 ave 3916 max 3916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 64308.0 ave 64308 max 64308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64308 Ave neighs/atom = 70.513158 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 8 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.701 | 4.701 | 4.701 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -3845.9634 -3845.9634 22.178819 77.864663 6.363273 544.71705 544.71705 506.01179 708.61515 419.52422 2.2688843 1944.8042 Loop time of 2.865e-06 on 1 procs for 0 steps with 912 atoms 209.4% CPU use with 1 MPI tasks x 1 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 | | 2.865e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3916.00 ave 3916 max 3916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 32154.0 ave 32154 max 32154 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 64308.0 ave 64308 max 64308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64308 Ave neighs/atom = 70.513158 Neighbor list builds = 0 Dangerous builds = 0 912 -3845.96334257528 eV 2.26888429526768 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01