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 -56.868488 0.0000000) to (34.824695 56.868488 8.8454813) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6168863 5.5034021 5.8969875 Created 1485 atoms using lattice units in orthogonal box = (0.0000000 -56.868488 0.0000000) to (34.824695 56.868488 8.8454813) create_atoms CPU = 0.003 seconds 1485 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6168863 5.5034021 5.8969875 Created 1491 atoms using lattice units in orthogonal box = (0.0000000 -56.868488 0.0000000) to (34.824695 56.868488 8.8454813) create_atoms CPU = 0.002 seconds 1491 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 = 14 43 4 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 = 2976 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 = 14 43 4 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) = 6.306 | 6.306 | 6.306 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12300.937 0 -12300.937 25519.519 44 0 -12609.133 0 -12609.133 2978.0596 Loop time of 10.421 on 1 procs for 44 steps with 2976 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 = -12300.9368478269 -12609.1209955886 -12609.1333540613 Force two-norm initial, final = 223.08583 0.43230096 Force max component initial, final = 31.171935 0.064877688 Final line search alpha, max atom move = 0.85967533 0.055773748 Iterations, force evaluations = 44 68 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.321 | 10.321 | 10.321 | 0.0 | 99.04 Neigh | 0.081601 | 0.081601 | 0.081601 | 0.0 | 0.78 Comm | 0.0063625 | 0.0063625 | 0.0063625 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01177 | | | 0.11 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6592.00 ave 6592 max 6592 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: 160712.0 ave 160712 max 160712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160712 Ave neighs/atom = 54.002688 Neighbor list builds = 2 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 = 14 43 4 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 : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.306 | 6.306 | 6.306 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -12609.133 0 -12609.133 2978.0596 35035.673 47 0 -12609.244 0 -12609.244 14.319293 35097.735 Loop time of 0.848804 on 1 procs for 3 steps with 2976 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 = -12609.1333540613 -12609.2437976353 -12609.2439855625 Force two-norm initial, final = 129.42027 1.6184411 Force max component initial, final = 112.58944 1.0733809 Final line search alpha, max atom move = 0.00019750217 0.00021199506 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.84631 | 0.84631 | 0.84631 | 0.0 | 99.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032992 | 0.00032992 | 0.00032992 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002169 | | | 0.26 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6592.00 ave 6592 max 6592 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: 160758.0 ave 160758 max 160758 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160758 Ave neighs/atom = 54.018145 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 = 14 43 4 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) = 6.444 | 6.444 | 6.444 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12609.244 0 -12609.244 14.319293 Loop time of 2.084e-06 on 1 procs for 0 steps with 2976 atoms 144.0% 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 | | 2.084e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6592.00 ave 6592 max 6592 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: 160736.0 ave 160736 max 160736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160736 Ave neighs/atom = 54.010753 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 = 14 43 4 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) = 6.444 | 6.444 | 6.444 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 -12609.244 -12609.244 34.889246 113.78271 8.8412006 14.319293 14.319293 33.104526 -39.121699 48.975051 2.3005702 944.79337 Loop time of 1.821e-06 on 1 procs for 0 steps with 2976 atoms 219.7% 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 | | 1.821e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6592.00 ave 6592 max 6592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 80368.0 ave 80368 max 80368 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 160736.0 ave 160736 max 160736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160736 Ave neighs/atom = 54.010753 Neighbor list builds = 0 Dangerous builds = 0 2976 -12609.2439855625 eV 2.30057020393811 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12