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 = 3.5200135 3.5200135 3.5200135 Created orthogonal box = (0.0000000 -42.536005 0.0000000) to (52.091443 42.536005 8.6222370) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9950699 5.2437310 5.7481580 Created 1758 atoms using lattice units in orthogonal box = (0.0000000 -42.536005 0.0000000) to (52.091443 42.536005 8.6222370) create_atoms CPU = 0.002 seconds 1758 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9950699 5.2437310 5.7481580 Created 1758 atoms using lattice units in orthogonal box = (0.0000000 -42.536005 0.0000000) to (52.091443 42.536005 8.6222370) create_atoms CPU = 0.002 seconds 1758 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 21 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 60 atoms, new total = 3456 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_871937946490_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.902 | 7.902 | 7.902 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15257.199 0 -15257.199 -1444.1155 47 0 -15320.008 0 -15320.008 -15161.216 Loop time of 2.87783 on 1 procs for 47 steps with 3456 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 = -15257.1992867011 -15319.9951505091 -15320.0083465225 Force two-norm initial, final = 27.069238 0.37243394 Force max component initial, final = 3.2976985 0.016133724 Final line search alpha, max atom move = 1.0000000 0.016133724 Iterations, force evaluations = 47 85 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8138 | 2.8138 | 2.8138 | 0.0 | 97.78 Neigh | 0.042017 | 0.042017 | 0.042017 | 0.0 | 1.46 Comm | 0.0095704 | 0.0095704 | 0.0095704 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01241 | | | 0.43 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12582.0 ave 12582 max 12582 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: 774000.0 ave 774000 max 774000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 774000 Ave neighs/atom = 223.95833 Neighbor list builds = 1 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.903 | 7.903 | 7.903 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -15320.008 0 -15320.008 -15161.216 38209.648 52 0 -15321.151 0 -15321.151 -3255.4803 37948.692 Loop time of 0.2615 on 1 procs for 5 steps with 3456 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 = -15320.0083465226 -15321.1484500195 -15321.1511770979 Force two-norm initial, final = 464.02959 0.53596527 Force max component initial, final = 352.33365 0.034904256 Final line search alpha, max atom move = 7.5839033e-05 2.6471050e-06 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25682 | 0.25682 | 0.25682 | 0.0 | 98.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069889 | 0.00069889 | 0.00069889 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003979 | | | 1.52 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12621.0 ave 12621 max 12621 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: 773316.0 ave 773316 max 773316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 773316 Ave neighs/atom = 223.76042 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 8.041 | 8.041 | 8.041 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15321.151 0 -15321.151 -3255.4803 Loop time of 1.813e-06 on 1 procs for 0 steps with 3456 atoms 110.3% 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 | | 1.813e-06 | | |100.00 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12648.0 ave 12648 max 12648 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: 774480.0 ave 774480 max 774480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 774480 Ave neighs/atom = 224.09722 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 8.041 | 8.041 | 8.041 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 -15321.151 -15321.151 51.874865 85.07201 8.5991026 -3255.4803 -3255.4803 1.0658153 -9766.4912 -1.0155501 2.2144679 1595.0304 Loop time of 2.653e-06 on 1 procs for 0 steps with 3456 atoms 226.2% 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 | | 2.653e-06 | | |100.00 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12648.0 ave 12648 max 12648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 387240.0 ave 387240 max 387240 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 774480.0 ave 774480 max 774480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 774480 Ave neighs/atom = 224.09722 Neighbor list builds = 0 Dangerous builds = 0 3456 -15226.9357726431 eV 2.2144679283831 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03