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 = 3.6784521 3.6784521 3.6784521 Created orthogonal box = (0.0000000 -70.372933 0.0000000) to (40.629832 70.372933 6.3712660) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9945654 5.3837217 6.3712660 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -70.372933 0.0000000) to (40.629832 70.372933 6.3712660) create_atoms CPU = 0.003 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9945654 5.3837217 6.3712660 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -70.372933 0.0000000) to (40.629832 70.372933 6.3712660) create_atoms CPU = 0.003 seconds 1466 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 14 46 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2930 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_024705128470_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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 14 46 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.781 | 5.781 | 5.781 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11960.206 0 -11960.206 23333.006 750 0 -12408.004 0 -12408.004 -54675.953 Loop time of 14.5398 on 1 procs for 750 steps with 2930 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11960.2058625831 -12407.9915262075 -12408.0035906807 Force two-norm initial, final = 263.86435 0.39690898 Force max component initial, final = 70.521191 0.10830017 Final line search alpha, max atom move = 1.0000000 0.10830017 Iterations, force evaluations = 750 1439 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.686 | 13.686 | 13.686 | 0.0 | 94.13 Neigh | 0.51128 | 0.51128 | 0.51128 | 0.0 | 3.52 Comm | 0.13972 | 0.13972 | 0.13972 | 0.0 | 0.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2029 | | | 1.40 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9215.00 ave 9215 max 9215 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: 192904.0 ave 192904 max 192904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192904 Ave neighs/atom = 65.837543 Neighbor list builds = 27 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 14 46 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 750 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.397 | 5.397 | 5.397 Mbytes Step Temp E_pair E_mol TotEng Press Volume 750 0 -12408.004 0 -12408.004 -54675.953 36433.963 769 0 -12433.505 0 -12433.505 -294.8557 35068.331 Loop time of 0.236519 on 1 procs for 19 steps with 2930 atoms 97.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12408.0035906806 -12433.4984362234 -12433.5050061882 Force two-norm initial, final = 2172.5337 13.068306 Force max component initial, final = 1450.8614 11.324556 Final line search alpha, max atom move = 4.5453842e-05 0.00051474458 Iterations, force evaluations = 19 20 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20473 | 0.20473 | 0.20473 | 0.0 | 86.56 Neigh | 0.018585 | 0.018585 | 0.018585 | 0.0 | 7.86 Comm | 0.0017956 | 0.0017956 | 0.0017956 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01141 | | | 4.82 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9319.00 ave 9319 max 9319 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: 195260.0 ave 195260 max 195260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 195260 Ave neighs/atom = 66.641638 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 13 46 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.916 | 5.916 | 5.916 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12433.505 0 -12433.505 -294.8557 Loop time of 2.497e-06 on 1 procs for 0 steps with 2930 atoms 160.2% 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 | | 2.497e-06 | | |100.00 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9354.00 ave 9354 max 9354 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: 201068.0 ave 201068 max 201068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201068 Ave neighs/atom = 68.623891 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 13 46 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.916 | 5.916 | 5.916 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 -12433.505 -12433.505 39.89057 139.03203 6.3230994 -294.8557 -294.8557 -507.9742 -212.666 -163.92691 2.2890212 4745.3576 Loop time of 5.798e-06 on 1 procs for 0 steps with 2930 atoms 189.7% 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 | | 5.798e-06 | | |100.00 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9354.00 ave 9354 max 9354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100534.0 ave 100534 max 100534 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 201068.0 ave 201068 max 201068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201068 Ave neighs/atom = 68.623891 Neighbor list builds = 0 Dangerous builds = 0 2930 -12433.5047131882 eV 2.28902117512215 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15