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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -42.753327 0.0000000) to (52.361918 42.753327 8.8507796) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9842192 5.4968563 5.9005197 Created 1663 atoms using lattice units in orthogonal box = (0.0000000 -42.753327 0.0000000) to (52.361918 42.753327 8.8507796) create_atoms CPU = 0.003 seconds 1663 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9842192 5.4968563 5.9005197 Created 1687 atoms using lattice units in orthogonal box = (0.0000000 -42.753327 0.0000000) to (52.361918 42.753327 8.8507796) create_atoms CPU = 0.003 seconds 1687 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 ghost atom cutoff = 6 binsize = 3, bins = 18 29 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3350 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_087820130586_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 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.637 | 5.637 | 5.637 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11258.101 0 -11258.101 40542.197 111 0 -11803.283 0 -11803.283 4030.3746 Loop time of 11.3319 on 1 procs for 111 steps with 3350 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11258.100562323 -11803.2712953937 -11803.283029696 Force two-norm initial, final = 534.01983 0.36640920 Force max component initial, final = 102.19742 0.082498523 Final line search alpha, max atom move = 1.0000000 0.082498523 Iterations, force evaluations = 111 193 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.221 | 11.221 | 11.221 | 0.0 | 99.02 Neigh | 0.047645 | 0.047645 | 0.047645 | 0.0 | 0.42 Comm | 0.024113 | 0.024113 | 0.024113 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03897 | | | 0.34 Nlocal: 3350.00 ave 3350 max 3350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7924.00 ave 7924 max 7924 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: 258528.0 ave 258528 max 258528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 258528 Ave neighs/atom = 77.172537 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 111 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.634 | 5.634 | 5.634 Mbytes Step Temp E_pair E_mol TotEng Press Volume 111 0 -11803.283 0 -11803.283 4030.3746 39627.528 115 0 -11803.624 0 -11803.624 -326.20533 39749.735 Loop time of 0.353527 on 1 procs for 4 steps with 3350 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 = -11803.283029696 -11803.6173853606 -11803.6238609738 Force two-norm initial, final = 207.37537 15.913253 Force max component initial, final = 164.40769 13.204885 Final line search alpha, max atom move = 4.6396380e-05 0.00061265885 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34981 | 0.34981 | 0.34981 | 0.0 | 98.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045485 | 0.00045485 | 0.00045485 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003263 | | | 0.92 Nlocal: 3350.00 ave 3350 max 3350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7559.00 ave 7559 max 7559 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: 258920.0 ave 258920 max 258920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 258920 Ave neighs/atom = 77.289552 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 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.772 | 5.772 | 5.772 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11803.624 0 -11803.624 -326.20533 Loop time of 2.51e-06 on 1 procs for 0 steps with 3350 atoms 199.2% 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 | | 2.51e-06 | | |100.00 Nlocal: 3350.00 ave 3350 max 3350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7559.00 ave 7559 max 7559 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: 258688.0 ave 258688 max 258688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 258688 Ave neighs/atom = 77.220299 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 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.772 | 5.772 | 5.772 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 -11803.624 -11803.624 52.447335 85.763821 8.8370374 -326.20533 -326.20533 -342.52251 -104.67592 -531.41756 2.2742994 1838.7132 Loop time of 2.672e-06 on 1 procs for 0 steps with 3350 atoms 336.8% 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 | | 2.672e-06 | | |100.00 Nlocal: 3350.00 ave 3350 max 3350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7559.00 ave 7559 max 7559 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 129344.0 ave 129344 max 129344 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 258688.0 ave 258688 max 258688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 258688 Ave neighs/atom = 77.220299 Neighbor list builds = 0 Dangerous builds = 0 3350 -11803.6238609738 eV 2.2742994442986 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12