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 = 2.8886457 2.8886457 2.8886457 Created orthogonal box = (0.0000000 -44.001429 0.0000000) to (21.999270 44.001429 2.8886457) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.7929776 3.7929776 2.8886457 Created 233 atoms using lattice units in orthogonal box = (0.0000000 -44.001429 0.0000000) to (21.999270 44.001429 2.8886457) create_atoms CPU = 0.002 seconds 233 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.7929776 3.7929776 2.8886457 Created 233 atoms using lattice units in orthogonal box = (0.0000000 -44.001429 0.0000000) to (21.999270 44.001429 2.8886457) create_atoms CPU = 0.001 seconds 233 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 33 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 3 atoms, new total = 463 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 33 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) = 4.829 | 4.829 | 4.829 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1878.5846 0 -1878.5846 26585.261 63 0 -1923.7858 0 -1923.7858 3913.2398 Loop time of 9.94116 on 1 procs for 63 steps with 463 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 = -1878.58461197662 -1923.78444784466 -1923.78578632212 Force two-norm initial, final = 92.047377 0.18922878 Force max component initial, final = 25.559907 0.073717982 Final line search alpha, max atom move = 1.0000000 0.073717982 Iterations, force evaluations = 63 120 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.9248 | 9.9248 | 9.9248 | 0.0 | 99.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0084667 | 0.0084667 | 0.0084667 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007902 | | | 0.08 Nlocal: 463.000 ave 463 max 463 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3051.00 ave 3051 max 3051 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: 26648.0 ave 26648 max 26648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26648 Ave neighs/atom = 57.555076 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 33 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 : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.829 | 4.829 | 4.829 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -1923.7858 0 -1923.7858 3913.2398 5592.4141 65 0 -1923.7896 0 -1923.7896 3959.1597 5591.9556 Loop time of 0.406757 on 1 procs for 2 steps with 463 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 = -1923.78578632212 -1923.78909016838 -1923.7895729059 Force two-norm initial, final = 5.4521435 0.20532285 Force max component initial, final = 4.4342059 0.077106196 Final line search alpha, max atom move = 0.00025856588 1.9937031e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40536 | 0.40536 | 0.40536 | 0.0 | 99.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032952 | 0.00032952 | 0.00032952 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001066 | | | 0.26 Nlocal: 463.000 ave 463 max 463 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2983.00 ave 2983 max 2983 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: 26600.0 ave 26600 max 26600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26600 Ave neighs/atom = 57.451404 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 33 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) = 4.967 | 4.967 | 4.967 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1923.7896 0 -1923.7896 3959.1597 Loop time of 6.314e-06 on 1 procs for 0 steps with 463 atoms 190.1% 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 | | 6.314e-06 | | |100.00 Nlocal: 463.000 ave 463 max 463 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2983.00 ave 2983 max 2983 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: 26600.0 ave 26600 max 26600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26600 Ave neighs/atom = 57.451404 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 33 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) = 4.967 | 4.967 | 4.967 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 -1923.7896 -1923.7896 22.020419 88.002858 2.8856348 3959.1597 3959.1597 -1.9523414 11876.933 2.4987716 2.3238865 310.63311 Loop time of 6.414e-06 on 1 procs for 0 steps with 463 atoms 265.0% 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 | | 6.414e-06 | | |100.00 Nlocal: 463.000 ave 463 max 463 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2983.00 ave 2983 max 2983 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13300.0 ave 13300 max 13300 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 26600.0 ave 26600 max 26600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26600 Ave neighs/atom = 57.451404 Neighbor list builds = 0 Dangerous builds = 0 463 -1923.7895729059 eV 2.32388649470253 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10