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 = 3.5242205 3.5242205 3.5242205 Created orthogonal box = (0.0000000 -38.605901 0.0000000) to (7.8803965 38.605901 8.6325418) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7282379 5.1474534 5.7550279 Created 240 atoms using lattice units in orthogonal box = (0.0000000 -38.605901 0.0000000) to (7.8803965 38.605901 8.6325418) create_atoms CPU = 0.002 seconds 240 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7282379 5.1474534 5.7550279 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -38.605901 0.0000000) to (7.8803965 38.605901 8.6325418) create_atoms CPU = 0.001 seconds 242 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 = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 3 25 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 6.3171695 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 480 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_769632475533_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 = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 3 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.3171695 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) = 4.480 | 4.480 | 4.480 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2031.5458 0 -2031.5458 77955.752 55 0 -2129.1305 0 -2129.1305 22943.775 Loop time of 0.646473 on 1 procs for 55 steps with 480 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 = -2031.54583559191 -2129.12880797241 -2129.13045970947 Force two-norm initial, final = 273.27949 0.16784534 Force max component initial, final = 85.433164 0.043247883 Final line search alpha, max atom move = 1.0000000 0.043247883 Iterations, force evaluations = 55 106 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.62895 | 0.62895 | 0.62895 | 0.0 | 97.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0089284 | 0.0089284 | 0.0089284 | 0.0 | 1.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00859 | | | 1.33 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3150.00 ave 3150 max 3150 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: 41648.0 ave 41648 max 41648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41648 Ave neighs/atom = 86.766667 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 = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 3 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.3171695 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.479 | 4.479 | 4.479 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -2129.1305 0 -2129.1305 22943.775 5252.5531 67 0 -2129.8378 0 -2129.8378 -109.15413 5308.1347 Loop time of 0.0708063 on 1 procs for 12 steps with 480 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 = -2129.13045970947 -2129.83599538905 -2129.83780638715 Force two-norm initial, final = 148.30570 0.81846341 Force max component initial, final = 132.39235 0.48101566 Final line search alpha, max atom move = 0.00026585952 0.00012788260 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.066332 | 0.066332 | 0.066332 | 0.0 | 93.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00086668 | 0.00086668 | 0.00086668 | 0.0 | 1.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003608 | | | 5.10 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3044.00 ave 3044 max 3044 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: 41260.0 ave 41260 max 41260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41260 Ave neighs/atom = 85.958333 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 = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 3 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.3171695 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) = 4.617 | 4.617 | 4.617 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2129.8378 0 -2129.8378 -109.15413 Loop time of 6.515e-06 on 1 procs for 0 steps with 480 atoms 184.2% 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 | | 6.515e-06 | | |100.00 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3021.00 ave 3021 max 3021 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: 41160.0 ave 41160 max 41160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41160 Ave neighs/atom = 85.750000 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 = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 3 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.3171695 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) = 4.617 | 4.617 | 4.617 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 -2129.8378 -2129.8378 7.8776113 78.11161 8.6264439 -109.15413 -109.15413 -145.13566 -124.67947 -57.647265 2.2179061 266.63923 Loop time of 6.374e-06 on 1 procs for 0 steps with 480 atoms 266.7% 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 | | 6.374e-06 | | |100.00 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3021.00 ave 3021 max 3021 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20580.0 ave 20580 max 20580 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 41160.0 ave 41160 max 41160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41160 Ave neighs/atom = 85.750000 Neighbor list builds = 0 Dangerous builds = 0 480 -2129.83780638715 eV 2.2179060852387 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01