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 -39.106161 0.0000000) to (39.102483 39.106161 3.6784521) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1905950 5.1905950 3.6784521 Created 453 atoms using lattice units in orthogonal box = (0.0000000 -39.106161 0.0000000) to (39.102483 39.106161 3.6784521) create_atoms CPU = 0.002 seconds 453 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1905950 5.1905950 3.6784521 Created 453 atoms using lattice units in orthogonal box = (0.0000000 -39.106161 0.0000000) to (39.102483 39.106161 3.6784521) create_atoms CPU = 0.001 seconds 453 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 = 13 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 4 atoms, new total = 902 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 = 13 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) = 4.556 | 4.556 | 4.556 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3740.0373 0 -3740.0373 20016.739 94 0 -3802.9632 0 -3802.9632 -4284.9008 Loop time of 1.05202 on 1 procs for 94 steps with 902 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 = -3740.03731808463 -3802.95958795874 -3802.96319097307 Force two-norm initial, final = 41.516044 0.20272113 Force max component initial, final = 10.418051 0.048973624 Final line search alpha, max atom move = 1.0000000 0.048973624 Iterations, force evaluations = 94 166 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0002 | 1.0002 | 1.0002 | 0.0 | 95.07 Neigh | 0.011723 | 0.011723 | 0.011723 | 0.0 | 1.11 Comm | 0.020308 | 0.020308 | 0.020308 | 0.0 | 1.93 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0198 | | | 1.88 Nlocal: 902.000 ave 902 max 902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5287.00 ave 5287 max 5287 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: 69702.0 ave 69702 max 69702 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69702 Ave neighs/atom = 77.274945 Neighbor list builds = 1 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 = 13 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 : 94 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.556 | 4.556 | 4.556 Mbytes Step Temp E_pair E_mol TotEng Press Volume 94 0 -3802.9632 0 -3802.9632 -4284.9008 11249.795 108 0 -3803.5599 0 -3803.5599 -4851.1558 11248.882 Loop time of 0.1081 on 1 procs for 14 steps with 902 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 = -3802.96319097306 -3803.5573061663 -3803.55985174728 Force two-norm initial, final = 77.106794 0.49858609 Force max component initial, final = 73.537043 0.10124154 Final line search alpha, max atom move = 0.00027193951 2.7531576e-05 Iterations, force evaluations = 14 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.099395 | 0.099395 | 0.099395 | 0.0 | 91.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017793 | 0.0017793 | 0.0017793 | 0.0 | 1.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006926 | | | 6.41 Nlocal: 902.000 ave 902 max 902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5311.00 ave 5311 max 5311 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: 70018.0 ave 70018 max 70018 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70018 Ave neighs/atom = 77.625277 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 = 13 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) = 4.694 | 4.694 | 4.694 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3803.5599 0 -3803.5599 -4851.1558 Loop time of 6.615e-06 on 1 procs for 0 steps with 902 atoms 181.4% 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 | | 6.615e-06 | | |100.00 Nlocal: 902.000 ave 902 max 902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5343.00 ave 5343 max 5343 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: 70062.0 ave 70062 max 70062 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70062 Ave neighs/atom = 77.674058 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 = 13 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) = 4.694 | 4.694 | 4.694 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 -3803.5599 -3803.5599 38.638609 78.212322 3.7223114 -4851.1558 -4851.1558 3.6586385 -14551.665 -5.4610698 2.3568548 161.31624 Loop time of 7.367e-06 on 1 procs for 0 steps with 902 atoms 271.5% 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 | | 7.367e-06 | | |100.00 Nlocal: 902.000 ave 902 max 902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5343.00 ave 5343 max 5343 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35031.0 ave 35031 max 35031 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 70062.0 ave 70062 max 70062 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70062 Ave neighs/atom = 77.674058 Neighbor list builds = 0 Dangerous builds = 0 902 -3803.55976154728 eV 2.35685475369861 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01