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 (27.771705 39.275121 5.2021169) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3338976 6.2013350 5.2021169 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -39.275121 0.0000000) to (27.771705 39.275121 5.2021169) create_atoms CPU = 0.004 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3338976 6.2013350 5.2021169 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -39.275121 0.0000000) to (27.771705 39.275121 5.2021169) create_atoms CPU = 0.003 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 = 10 26 2 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 0 atoms, new total = 914 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 = 10 26 2 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) = 4.561 | 4.561 | 4.561 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3644.7643 0 -3644.7643 34491.406 420 0 -3868.3887 0 -3868.3887 -54474.097 Loop time of 5.10392 on 1 procs for 420 steps with 914 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 = -3644.76434447092 -3868.38518994772 -3868.38866240457 Force two-norm initial, final = 208.14625 0.19496005 Force max component initial, final = 44.793126 0.050480357 Final line search alpha, max atom move = 0.91597793 0.046238893 Iterations, force evaluations = 420 782 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7616 | 4.7616 | 4.7616 | 0.0 | 93.29 Neigh | 0.16316 | 0.16316 | 0.16316 | 0.0 | 3.20 Comm | 0.088252 | 0.088252 | 0.088252 | 0.0 | 1.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.09087 | | | 1.78 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4252.00 ave 4252 max 4252 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: 60700.0 ave 60700 max 60700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60700 Ave neighs/atom = 66.411379 Neighbor list builds = 14 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 = 10 26 2 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 : 420 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.569 | 4.569 | 4.569 Mbytes Step Temp E_pair E_mol TotEng Press Volume 420 0 -3868.3887 0 -3868.3887 -54474.097 11348.284 460 0 -3883.685 0 -3883.685 -29.846531 10905.411 Loop time of 0.294568 on 1 procs for 40 steps with 914 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3868.38866240457 -3883.68199175686 -3883.68501543127 Force two-norm initial, final = 791.96356 1.6380415 Force max component initial, final = 730.30239 0.57266767 Final line search alpha, max atom move = 0.00013530070 7.7482335e-05 Iterations, force evaluations = 40 41 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27355 | 0.27355 | 0.27355 | 0.0 | 92.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0040058 | 0.0040058 | 0.0040058 | 0.0 | 1.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01701 | | | 5.77 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4284.00 ave 4284 max 4284 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: 60476.0 ave 60476 max 60476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60476 Ave neighs/atom = 66.166302 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 = 10 26 2 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) = 4.708 | 4.708 | 4.708 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3883.685 0 -3883.685 -29.846531 Loop time of 6.405e-06 on 1 procs for 0 steps with 914 atoms 187.4% 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 | | 6.405e-06 | | |100.00 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4412.00 ave 4412 max 4412 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: 61508.0 ave 61508 max 61508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61508 Ave neighs/atom = 67.295405 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 = 10 26 2 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) = 4.708 | 4.708 | 4.708 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 -3883.685 -3883.685 27.822924 78.442344 4.9967624 -29.846531 -29.846531 -84.289062 -2.6111006 -2.6394311 2.3390913 1724.8817 Loop time of 3.4309e-05 on 1 procs for 0 steps with 914 atoms 137.0% 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 | | 3.431e-05 | | |100.00 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4412.00 ave 4412 max 4412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30754.0 ave 30754 max 30754 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 61508.0 ave 61508 max 61508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61508 Ave neighs/atom = 67.295405 Neighbor list builds = 0 Dangerous builds = 0 914 -3883.68492403127 eV 2.3390913005437 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05