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 = 3.7004755 3.7004755 3.7004755 Created orthogonal box = (0.0000000 -57.803276 0.0000000) to (28.901638 57.803276 3.7004755) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2117708 5.2117708 3.7004755 Created 487 atoms using lattice units in orthogonal box = (0.0000000 -57.803276 0.0000000) to (28.901638 57.803276 3.7004755) create_atoms CPU = 0.001 seconds 487 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2117708 5.2117708 3.7004755 Created 489 atoms using lattice units in orthogonal box = (0.0000000 -57.803276 0.0000000) to (28.901638 57.803276 3.7004755) create_atoms CPU = 0.001 seconds 489 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 8 30 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 7.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 976 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_466808877130_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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 8 30 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 5.023 | 5.023 | 5.023 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3671.0594 0 -3671.0594 66688.391 405 0 -3907.2056 0 -3907.2056 -17251.198 Loop time of 6.40538 on 1 procs for 405 steps with 976 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3671.05941805267 -3907.20189515275 -3907.20560298653 Force two-norm initial, final = 291.67489 0.19375327 Force max component initial, final = 57.340777 0.022272335 Final line search alpha, max atom move = 1.0000000 0.022272335 Iterations, force evaluations = 405 795 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.2511 | 6.2511 | 6.2511 | 0.0 | 97.59 Neigh | 0.05203 | 0.05203 | 0.05203 | 0.0 | 0.81 Comm | 0.06373 | 0.06373 | 0.06373 | 0.0 | 0.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03857 | | | 0.60 Nlocal: 976.000 ave 976 max 976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8395.00 ave 8395 max 8395 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: 146078.0 ave 146078 max 146078 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146078 Ave neighs/atom = 149.67008 Neighbor list builds = 6 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 8 30 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 405 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.030 | 5.030 | 5.030 Mbytes Step Temp E_pair E_mol TotEng Press Volume 405 0 -3907.2056 0 -3907.2056 -17251.198 12364.098 446 0 -3924.2929 0 -3924.2929 30.5048 12100.821 Loop time of 0.373471 on 1 procs for 41 steps with 976 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 = -3907.20560298654 -3924.28947548077 -3924.29287076734 Force two-norm initial, final = 579.26527 4.5454665 Force max component initial, final = 365.06903 2.3700368 Final line search alpha, max atom move = 0.00023259985 0.00055127021 Iterations, force evaluations = 41 42 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33242 | 0.33242 | 0.33242 | 0.0 | 89.01 Neigh | 0.025819 | 0.025819 | 0.025819 | 0.0 | 6.91 Comm | 0.0031642 | 0.0031642 | 0.0031642 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01207 | | | 3.23 Nlocal: 976.000 ave 976 max 976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8468.00 ave 8468 max 8468 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: 151250.0 ave 151250 max 151250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 151250 Ave neighs/atom = 154.96926 Neighbor list builds = 3 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 8 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 5.168 | 5.168 | 5.168 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3924.2929 0 -3924.2929 30.5048 Loop time of 1.608e-06 on 1 procs for 0 steps with 976 atoms 124.4% 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 | | 1.608e-06 | | |100.00 Nlocal: 976.000 ave 976 max 976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8485.00 ave 8485 max 8485 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: 152336.0 ave 152336 max 152336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 152336 Ave neighs/atom = 156.08197 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 8 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 5.168 | 5.168 | 5.168 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 -3924.2929 -3924.2929 28.212974 111.61068 3.8429099 30.5048 30.5048 -33.974472 302.95208 -177.4632 2.300493 212.79678 Loop time of 1.825e-06 on 1 procs for 0 steps with 976 atoms 219.2% 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 | | 1.825e-06 | | |100.00 Nlocal: 976.000 ave 976 max 976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8485.00 ave 8485 max 8485 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 76168.0 ave 76168 max 76168 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 152336.0 ave 152336 max 152336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 152336 Ave neighs/atom = 156.08197 Neighbor list builds = 0 Dangerous builds = 0 976 -3924.29287076734 eV 2.3004929806322 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07