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 -39.275121 0.0000000) to (27.771705 39.275121 5.2021169) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3594518 6.2013350 5.2021169 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -39.275121 0.0000000) to (27.771705 39.275121 5.2021169) create_atoms CPU = 0.004 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3594518 6.2013350 5.2021169 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -39.275121 0.0000000) to (27.771705 39.275121 5.2021169) create_atoms CPU = 0.003 seconds 458 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 = 10 26 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 910 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 = 10 26 2 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) = 4.561 | 4.561 | 4.561 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3586.726 0 -3586.726 32698.082 711 0 -3852.5589 0 -3852.5589 -64533.01 Loop time of 9.02615 on 1 procs for 711 steps with 910 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 = -3586.72600732462 -3852.55504496015 -3852.55887493162 Force two-norm initial, final = 252.09862 0.20867514 Force max component initial, final = 55.108260 0.032543876 Final line search alpha, max atom move = 1.0000000 0.032543876 Iterations, force evaluations = 711 1333 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.4414 | 8.4414 | 8.4414 | 0.0 | 93.52 Neigh | 0.27356 | 0.27356 | 0.27356 | 0.0 | 3.03 Comm | 0.15205 | 0.15205 | 0.15205 | 0.0 | 1.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1592 | | | 1.76 Nlocal: 910.000 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4187.00 ave 4187 max 4187 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: 60356.0 ave 60356 max 60356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60356 Ave neighs/atom = 66.325275 Neighbor list builds = 23 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 = 10 26 2 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 : 711 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.562 | 4.562 | 4.562 Mbytes Step Temp E_pair E_mol TotEng Press Volume 711 0 -3852.5589 0 -3852.5589 -64533.01 11348.284 753 0 -3870.799 0 -3870.799 -30.284597 10831.5 Loop time of 0.307827 on 1 procs for 42 steps with 910 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3852.55887493161 -3870.79840449214 -3870.79896745146 Force two-norm initial, final = 894.74758 1.3136218 Force max component initial, final = 794.39370 0.56158098 Final line search alpha, max atom move = 0.00036813727 0.00020673889 Iterations, force evaluations = 42 43 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2861 | 0.2861 | 0.2861 | 0.0 | 92.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0040989 | 0.0040989 | 0.0040989 | 0.0 | 1.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01763 | | | 5.73 Nlocal: 910.000 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4192.00 ave 4192 max 4192 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: 60412.0 ave 60412 max 60412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60412 Ave neighs/atom = 66.386813 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 = 9 26 2 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) = 4.701 | 4.701 | 4.701 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3870.799 0 -3870.799 -30.284597 Loop time of 6.184e-06 on 1 procs for 0 steps with 910 atoms 177.9% 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 | | 6.184e-06 | | |100.00 Nlocal: 910.000 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4362.00 ave 4362 max 4362 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: 61628.0 ave 61628 max 61628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61628 Ave neighs/atom = 67.723077 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 = 9 26 2 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) = 4.701 | 4.701 | 4.701 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 -3870.799 -3870.799 27.574664 78.741826 4.9885333 -30.284597 -30.284597 -15.184097 -83.270678 7.6009853 2.3215481 1173.8207 Loop time of 6.665e-06 on 1 procs for 0 steps with 910 atoms 270.1% 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 | | 6.665e-06 | | |100.00 Nlocal: 910.000 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4362.00 ave 4362 max 4362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30814.0 ave 30814 max 30814 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 61628.0 ave 61628 max 61628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61628 Ave neighs/atom = 67.723077 Neighbor list builds = 0 Dangerous builds = 0 910 -3870.79887645146 eV 2.32154805914502 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09