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 = 3.5600001 3.5600001 3.5600001 Created orthogonal box = (0.0000000 -36.305020 0.0000000) to (31.441070 36.305020 6.1661011) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6432689 5.5853877 6.1661011 Created 621 atoms using lattice units in orthogonal box = (0.0000000 -36.305020 0.0000000) to (31.441070 36.305020 6.1661011) create_atoms CPU = 0.001 seconds 621 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6432689 5.5853877 6.1661011 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -36.305020 0.0000000) to (31.441070 36.305020 6.1661011) create_atoms CPU = 0.001 seconds 629 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 19 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 1249 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.455 | 5.455 | 5.455 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5052.8836 0 -5052.8836 78973.628 114 0 -5458.8452 0 -5458.8452 25698.815 Loop time of 2.53232 on 1 procs for 114 steps with 1249 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 = -5052.88363775779 -5458.83975686536 -5458.84520279664 Force two-norm initial, final = 610.51564 0.36623134 Force max component initial, final = 138.18027 0.14072291 Final line search alpha, max atom move = 1.0000000 0.14072291 Iterations, force evaluations = 114 212 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4452 | 2.4452 | 2.4452 | 0.0 | 96.56 Neigh | 0.05628 | 0.05628 | 0.05628 | 0.0 | 2.22 Comm | 0.016705 | 0.016705 | 0.016705 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01415 | | | 0.56 Nlocal: 1249.00 ave 1249 max 1249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7057.00 ave 7057 max 7057 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: 218202.0 ave 218202 max 218202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 218202 Ave neighs/atom = 174.70136 Neighbor list builds = 4 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 114 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.455 | 5.455 | 5.455 Mbytes Step Temp E_pair E_mol TotEng Press Volume 114 0 -5458.8452 0 -5458.8452 25698.815 14076.822 125 0 -5460.5647 0 -5460.5647 15.216375 14234.52 Loop time of 0.150121 on 1 procs for 11 steps with 1249 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 = -5458.84520279664 -5460.56398150783 -5460.56469212867 Force two-norm initial, final = 415.17182 1.6974588 Force max component initial, final = 335.72975 0.94813471 Final line search alpha, max atom move = 0.00014165928 0.00013431208 Iterations, force evaluations = 11 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14585 | 0.14585 | 0.14585 | 0.0 | 97.16 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0007207 | 0.0007207 | 0.0007207 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003548 | | | 2.36 Nlocal: 1249.00 ave 1249 max 1249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7060.00 ave 7060 max 7060 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: 218210.0 ave 218210 max 218210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 218210 Ave neighs/atom = 174.70777 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.593 | 5.593 | 5.593 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5460.5647 0 -5460.5647 15.216375 Loop time of 1.699e-06 on 1 procs for 0 steps with 1249 atoms 117.7% 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 | | 1.699e-06 | | |100.00 Nlocal: 1249.00 ave 1249 max 1249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7008.00 ave 7008 max 7008 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: 217440.0 ave 217440 max 217440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 217440 Ave neighs/atom = 174.09127 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.593 | 5.593 | 5.593 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 -5460.5647 -5460.5647 31.497782 73.327219 6.1630773 15.216375 15.216375 -63.013022 1.9964987 106.66565 2.3225313 940.55792 Loop time of 3.615e-06 on 1 procs for 0 steps with 1249 atoms 221.3% 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 | | 3.615e-06 | | |100.00 Nlocal: 1249.00 ave 1249 max 1249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7008.00 ave 7008 max 7008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 108720.0 ave 108720 max 108720 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 217440.0 ave 217440 max 217440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 217440 Ave neighs/atom = 174.09127 Neighbor list builds = 0 Dangerous builds = 0 1249 -5460.56469212867 eV 2.32253125722051 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03