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 -42.826333 0.0000000) to (21.411406 42.826333 3.5200135) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0508066 4.0508066 3.5200135 Created 298 atoms using lattice units in orthogonal box = (0.0000000 -42.826333 0.0000000) to (21.411406 42.826333 3.5200135) create_atoms CPU = 0.001 seconds 298 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0508066 4.0508066 3.5200135 Created 298 atoms using lattice units in orthogonal box = (0.0000000 -42.826333 0.0000000) to (21.411406 42.826333 3.5200135) create_atoms CPU = 0.000 seconds 298 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 = 6 21 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 588 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 = 6 21 1 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) = 4.936 | 4.936 | 4.936 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2590.5026 0 -2590.5026 7186.328 38 0 -2604.3681 0 -2604.3681 -4155.6817 Loop time of 0.531554 on 1 procs for 38 steps with 588 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 = -2590.50259953449 -2604.36567585299 -2604.36813321321 Force two-norm initial, final = 17.175538 0.17289486 Force max component initial, final = 4.2549253 0.025431165 Final line search alpha, max atom move = 1.0000000 0.025431165 Iterations, force evaluations = 38 70 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.52389 | 0.52389 | 0.52389 | 0.0 | 98.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0046505 | 0.0046505 | 0.0046505 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003013 | | | 0.57 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6373.00 ave 6373 max 6373 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: 131364.0 ave 131364 max 131364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 131364 Ave neighs/atom = 223.40816 Neighbor list builds = 0 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 = 6 21 1 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 : 38 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.936 | 4.936 | 4.936 Mbytes Step Temp E_pair E_mol TotEng Press Volume 38 0 -2604.3681 0 -2604.3681 -4155.6817 6455.5077 40 0 -2604.3716 0 -2604.3716 -2529.1937 6449.5692 Loop time of 0.038163 on 1 procs for 2 steps with 588 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 = -2604.36813321322 -2604.37156231692 -2604.3716347993 Force two-norm initial, final = 10.334941 0.17981508 Force max component initial, final = 8.0403262 0.043092712 Final line search alpha, max atom move = 0.0019635362 8.4614098e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.036784 | 0.036784 | 0.036784 | 0.0 | 96.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028152 | 0.00028152 | 0.00028152 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001098 | | | 2.88 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6318.00 ave 6318 max 6318 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: 132012.0 ave 132012 max 132012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 132012 Ave neighs/atom = 224.51020 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 = 6 21 1 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) = 5.074 | 5.074 | 5.074 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2604.3716 0 -2604.3716 -2529.1937 Loop time of 2.072e-06 on 1 procs for 0 steps with 588 atoms 144.8% 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 | | 2.072e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6318.00 ave 6318 max 6318 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: 132060.0 ave 132060 max 132060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 132060 Ave neighs/atom = 224.59184 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 = 6 21 1 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) = 5.074 | 5.074 | 5.074 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 -2604.3716 -2604.3716 21.397512 85.652665 3.519059 -2529.1937 -2529.1937 4.1669544 -7581.0459 -10.702018 2.2621077 181.63167 Loop time of 2.321e-06 on 1 procs for 0 steps with 588 atoms 215.4% 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 | | 2.321e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6318.00 ave 6318 max 6318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 66030.0 ave 66030 max 66030 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 132060.0 ave 132060 max 132060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 132060 Ave neighs/atom = 224.59184 Neighbor list builds = 0 Dangerous builds = 0 588 -2588.34193056914 eV 2.26210765042167 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00