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 = 3.6063026 3.6063026 3.6063026 Created orthogonal box = (0.0000000 -40.800656 0.0000000) to (17.667202 40.800656 6.2462993) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8890675 5.1000820 6.2462993 Created 384 atoms using lattice units in orthogonal box = (0.0000000 -40.800656 0.0000000) to (17.667202 40.800656 6.2462993) create_atoms CPU = 0.001 seconds 384 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8890675 5.1000820 6.2462993 Created 396 atoms using lattice units in orthogonal box = (0.0000000 -40.800656 0.0000000) to (17.667202 40.800656 6.2462993) create_atoms CPU = 0.001 seconds 396 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 = 3 14 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, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 776 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 = 3 14 2 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) = 6.263 | 6.263 | 6.263 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2701.8969 0 -2701.8969 129012.77 210 0 -3239.5811 0 -3239.5811 25566.649 Loop time of 9.76655 on 1 procs for 210 steps with 776 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2701.89692307825 -3239.5780247703 -3239.58111901805 Force two-norm initial, final = 601.35038 0.24051419 Force max component initial, final = 170.66527 0.028053669 Final line search alpha, max atom move = 1.0000000 0.028053669 Iterations, force evaluations = 210 409 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.6334 | 9.6334 | 9.6334 | 0.0 | 98.64 Neigh | 0.05308 | 0.05308 | 0.05308 | 0.0 | 0.54 Comm | 0.043323 | 0.043323 | 0.043323 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03678 | | | 0.38 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11006.0 ave 11006 max 11006 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: 481520.0 ave 481520 max 481520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 481520 Ave neighs/atom = 620.51546 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 = 3 14 2 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 : 210 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.278 | 6.278 | 6.278 Mbytes Step Temp E_pair E_mol TotEng Press Volume 210 0 -3239.5811 0 -3239.5811 25566.649 9005.083 223 0 -3241.2776 0 -3241.2776 -46.152065 9135.3879 Loop time of 0.357777 on 1 procs for 13 steps with 776 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 = -3239.58111901807 -3241.2775723301 -3241.27763132788 Force two-norm initial, final = 282.87822 0.90186858 Force max component initial, final = 228.17734 0.31156737 Final line search alpha, max atom move = 0.00091554135 0.00028525281 Iterations, force evaluations = 13 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.3263 | 0.3263 | 0.3263 | 0.0 | 91.20 Neigh | 0.024843 | 0.024843 | 0.024843 | 0.0 | 6.94 Comm | 0.0014379 | 0.0014379 | 0.0014379 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005193 | | | 1.45 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10987.0 ave 10987 max 10987 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: 474704.0 ave 474704 max 474704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 474704 Ave neighs/atom = 611.73196 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 = 3 14 2 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) = 6.416 | 6.416 | 6.416 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3241.2776 0 -3241.2776 -46.152065 Loop time of 1.797e-06 on 1 procs for 0 steps with 776 atoms 166.9% 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 | | 1.797e-06 | | |100.00 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10987.0 ave 10987 max 10987 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: 475692.0 ave 475692 max 475692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 475692 Ave neighs/atom = 613.00515 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 = 3 14 2 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) = 6.416 | 6.416 | 6.416 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 -3241.2776 -3241.2776 17.617053 82.553302 6.2814409 -46.152065 -46.152065 -29.787582 -55.280587 -53.388026 2.3796037 597.18512 Loop time of 2.231e-06 on 1 procs for 0 steps with 776 atoms 224.1% 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 | | 2.231e-06 | | |100.00 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10987.0 ave 10987 max 10987 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 237846.0 ave 237846 max 237846 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 475692.0 ave 475692 max 475692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 475692 Ave neighs/atom = 613.00515 Neighbor list builds = 0 Dangerous builds = 0 776 -3241.27763132788 eV 2.37960374309402 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10