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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -52.111839 0.0000000) to (42.549138 52.111839 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2457842 4.9970257 5.7504086 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -52.111839 0.0000000) to (42.549138 52.111839 8.6256130) create_atoms CPU = 0.003 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2457842 4.9970257 5.7504086 Created 1758 atoms using lattice units in orthogonal box = (0.0000000 -52.111839 0.0000000) to (42.549138 52.111839 8.6256130) create_atoms CPU = 0.002 seconds 1758 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 34 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 3486 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 34 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 6.108 | 6.108 | 6.108 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14181.627 0 -14181.627 114802.86 156 0 -15451.235 0 -15451.235 886.40085 Loop time of 38.0468 on 1 procs for 156 steps with 3486 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 = -14181.6271768465 -15451.221829719 -15451.2346949403 Force two-norm initial, final = 2186.9633 0.43735471 Force max component initial, final = 310.43153 0.099343579 Final line search alpha, max atom move = 1.0000000 0.099343579 Iterations, force evaluations = 156 298 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 37.88 | 37.88 | 37.88 | 0.0 | 99.56 Neigh | 0.075274 | 0.075274 | 0.075274 | 0.0 | 0.20 Comm | 0.036385 | 0.036385 | 0.036385 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05519 | | | 0.15 Nlocal: 3486.00 ave 3486 max 3486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8837.00 ave 8837 max 8837 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: 298578.0 ave 298578 max 298578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 298578 Ave neighs/atom = 85.650602 Neighbor list builds = 3 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 34 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 156 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.108 | 6.108 | 6.108 Mbytes Step Temp E_pair E_mol TotEng Press Volume 156 0 -15451.235 0 -15451.235 886.40085 38251.382 160 0 -15451.476 0 -15451.476 -59.007344 38270.839 Loop time of 0.861455 on 1 procs for 4 steps with 3486 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 = -15451.2346949404 -15451.4758029378 -15451.4760365739 Force two-norm initial, final = 150.01492 2.7471372 Force max component initial, final = 139.88750 2.0052083 Final line search alpha, max atom move = 0.00019486716 0.00039074925 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.85695 | 0.85695 | 0.85695 | 0.0 | 99.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00057718 | 0.00057718 | 0.00057718 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003924 | | | 0.46 Nlocal: 3486.00 ave 3486 max 3486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9074.00 ave 9074 max 9074 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: 298614.0 ave 298614 max 298614 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 298614 Ave neighs/atom = 85.660929 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 34 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 6.246 | 6.246 | 6.246 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15451.476 0 -15451.476 -59.007344 Loop time of 2.999e-06 on 1 procs for 0 steps with 3486 atoms 166.7% 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 | | 2.999e-06 | | |100.00 Nlocal: 3486.00 ave 3486 max 3486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9064.00 ave 9064 max 9064 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: 298510.0 ave 298510 max 298510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 298510 Ave neighs/atom = 85.631096 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 34 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 6.246 | 6.246 | 6.246 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 -15451.476 -15451.476 42.485378 104.51852 8.6185704 -59.007344 -59.007344 -83.820566 -71.665278 -21.536188 2.2107208 1657.8485 Loop time of 3.463e-06 on 1 procs for 0 steps with 3486 atoms 231.0% 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 | | 3.463e-06 | | |100.00 Nlocal: 3486.00 ave 3486 max 3486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9064.00 ave 9064 max 9064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 149255.0 ave 149255 max 149255 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 298510.0 ave 298510 max 298510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 298510 Ave neighs/atom = 85.631096 Neighbor list builds = 0 Dangerous builds = 0 3486 -15451.4760365739 eV 2.21072077411102 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:39