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 = 3.6111526 3.6111526 3.6111526 Created orthogonal box = (0.0000000 -47.221948 0.0000000) to (22.260640 47.221948 5.1069410) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6864505 5.7991866 5.1069410 Created 450 atoms using lattice units in orthogonal box = (0.0000000 -47.221948 0.0000000) to (22.260640 47.221948 5.1069410) create_atoms CPU = 0.001 seconds 450 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6864505 5.7991866 5.1069410 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -47.221948 0.0000000) to (22.260640 47.221948 5.1069410) 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 36 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 908 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_137964310702_004#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.940 | 4.940 | 4.940 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3529.2996 0 -3529.2996 54920.106 70 0 -3840.9695 0 -3840.9695 -1888.3646 Loop time of 6.06559 on 1 procs for 70 steps with 908 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3529.29964809451 -3840.96571543678 -3840.96947003389 Force two-norm initial, final = 421.59967 0.24273935 Force max component initial, final = 70.647207 0.044136062 Final line search alpha, max atom move = 1.0000000 0.044136062 Iterations, force evaluations = 70 128 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.0537 | 6.0537 | 6.0537 | 0.0 | 99.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0049086 | 0.0049086 | 0.0049086 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007013 | | | 0.12 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3598.00 ave 3598 max 3598 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: 48868.0 ave 48868 max 48868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48868 Ave neighs/atom = 53.819383 Neighbor list builds = 0 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.324 | 5.324 | 5.324 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -3840.9695 0 -3840.9695 -1888.3646 10736.739 76 0 -3841.0817 0 -3841.0817 1.4744645 10725.192 Loop time of 0.40412 on 1 procs for 6 steps with 908 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3840.96947003388 -3841.08111750914 -3841.08170295212 Force two-norm initial, final = 43.181736 0.51026449 Force max component initial, final = 41.279766 0.10839504 Final line search alpha, max atom move = 0.00014227912 1.5422350e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40227 | 0.40227 | 0.40227 | 0.0 | 99.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028735 | 0.00028735 | 0.00028735 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001561 | | | 0.39 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3936.00 ave 3936 max 3936 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: 48808.0 ave 48808 max 48808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48808 Ave neighs/atom = 53.753304 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.462 | 5.462 | 5.462 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3841.0817 0 -3841.0817 1.4744645 Loop time of 2.302e-06 on 1 procs for 0 steps with 908 atoms 217.2% 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 | | 2.302e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3925.00 ave 3925 max 3925 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: 48816.0 ave 48816 max 48816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48816 Ave neighs/atom = 53.762115 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.462 | 5.462 | 5.462 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 -3841.0817 -3841.0817 22.148439 94.68298 5.1143453 1.4744645 1.4744645 6.1849601 1.2865031 -3.0480697 2.2421805 287.02761 Loop time of 2.211e-06 on 1 procs for 0 steps with 908 atoms 271.4% 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 | | 2.211e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3925.00 ave 3925 max 3925 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24408.0 ave 24408 max 24408 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 48816.0 ave 48816 max 48816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48816 Ave neighs/atom = 53.762115 Neighbor list builds = 0 Dangerous builds = 0 908 -3841.08170295212 eV 2.24218052877294 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06