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 = 2.8638485 2.8638485 2.8638485 Created orthogonal box = (0.0000000 -44.734744 0.0000000) to (22.367372 44.734744 2.8638485) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0334605 4.0334605 2.8638485 Created 244 atoms using lattice units in orthogonal box = (0.0000000 -44.734744 0.0000000) to (22.367372 44.734744 2.8638485) create_atoms CPU = 0.002 seconds 244 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0334605 4.0334605 2.8638485 Created 245 atoms using lattice units in orthogonal box = (0.0000000 -44.734744 0.0000000) to (22.367372 44.734744 2.8638485) create_atoms CPU = 0.001 seconds 245 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 4 15 1 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 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 486 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_147603128437_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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 4 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 5.381 | 5.381 | 5.381 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1665.2675 0 -1665.2675 85642.012 117 0 -2024.3957 0 -2024.3957 -2908.3262 Loop time of 8.91101 on 1 procs for 117 steps with 486 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 = -1665.26750731218 -2024.39377504194 -2024.39565767427 Force two-norm initial, final = 773.63026 0.19179953 Force max component initial, final = 353.44044 0.039382810 Final line search alpha, max atom move = 1.0000000 0.039382810 Iterations, force evaluations = 117 211 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.7631 | 8.7631 | 8.7631 | 0.0 | 98.34 Neigh | 0.069125 | 0.069125 | 0.069125 | 0.0 | 0.78 Comm | 0.05629 | 0.05629 | 0.05629 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02255 | | | 0.25 Nlocal: 486.000 ave 486 max 486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11635.0 ave 11635 max 11635 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: 293464.0 ave 293464 max 293464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 293464 Ave neighs/atom = 603.83539 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 4 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 117 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.381 | 5.381 | 5.381 Mbytes Step Temp E_pair E_mol TotEng Press Volume 117 0 -2024.3957 0 -2024.3957 -2908.3262 5731.1259 157 0 -2026.3304 0 -2026.3304 -1102.2797 5722.1895 Loop time of 1.83965 on 1 procs for 40 steps with 486 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 = -2024.39565767428 -2026.32898245622 -2026.33041975174 Force two-norm initial, final = 73.809970 6.9852507 Force max component initial, final = 66.343502 4.1556513 Final line search alpha, max atom move = 0.0038721608 0.016091350 Iterations, force evaluations = 40 41 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7677 | 1.7677 | 1.7677 | 0.0 | 96.09 Neigh | 0.033093 | 0.033093 | 0.033093 | 0.0 | 1.80 Comm | 0.010824 | 0.010824 | 0.010824 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02801 | | | 1.52 Nlocal: 486.000 ave 486 max 486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11542.0 ave 11542 max 11542 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: 294338.0 ave 294338 max 294338 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 294338 Ave neighs/atom = 605.63374 Neighbor list builds = 1 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 4 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 5.519 | 5.519 | 5.519 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2026.3304 0 -2026.3304 -1102.2797 Loop time of 6.605e-06 on 1 procs for 0 steps with 486 atoms 181.7% 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 | | 6.605e-06 | | |100.00 Nlocal: 486.000 ave 486 max 486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11502.0 ave 11502 max 11502 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: 293262.0 ave 293262 max 293262 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 293262 Ave neighs/atom = 603.41975 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 4 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 5.519 | 5.519 | 5.519 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 -2026.3304 -2026.3304 22.820861 91.085473 2.7528407 -1102.2797 -1102.2797 -1187.1464 -1113.8969 -1005.7956 2.3914615 123.16746 Loop time of 7.087e-06 on 1 procs for 0 steps with 486 atoms 296.3% 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 | | 7.087e-06 | | |100.00 Nlocal: 486.000 ave 486 max 486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11502.0 ave 11502 max 11502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 146631.0 ave 146631 max 146631 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 293262.0 ave 293262 max 293262 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 293262 Ave neighs/atom = 603.41975 Neighbor list builds = 0 Dangerous builds = 0 486 -2026.33041975173 eV 2.39146151748494 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11