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 = 2.8886457 2.8886457 2.8886457 Created orthogonal box = (0.0000000 -39.715201 0.0000000) to (10.808322 39.715201 7.0757080) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6321382 4.4124792 4.7171386 Created 254 atoms using lattice units in orthogonal box = (0.0000000 -39.715201 0.0000000) to (10.808322 39.715201 7.0757080) create_atoms CPU = 0.001 seconds 254 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6321382 4.4124792 4.7171386 Created 254 atoms using lattice units in orthogonal box = (0.0000000 -39.715201 0.0000000) to (10.808322 39.715201 7.0757080) create_atoms CPU = 0.000 seconds 254 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 30 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 4 atoms, new total = 504 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.838 | 4.838 | 4.838 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2044.4243 0 -2044.4243 29963.115 50 0 -2093.2723 0 -2093.2723 5182.2649 Loop time of 3.68911 on 1 procs for 50 steps with 504 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2044.4243486199 -2093.27026198153 -2093.27234769829 Force two-norm initial, final = 86.206380 0.19572507 Force max component initial, final = 26.432262 0.021532924 Final line search alpha, max atom move = 1.0000000 0.021532924 Iterations, force evaluations = 50 96 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.684 | 3.684 | 3.684 | 0.0 | 99.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0024114 | 0.0024114 | 0.0024114 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002717 | | | 0.07 Nlocal: 504.000 ave 504 max 504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2536.00 ave 2536 max 2536 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: 29032.0 ave 29032 max 29032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29032 Ave neighs/atom = 57.603175 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.836 | 4.836 | 4.836 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -2093.2723 0 -2093.2723 5182.2649 6074.5618 52 0 -2093.2763 0 -2093.2763 5162.3166 6074.687 Loop time of 0.157237 on 1 procs for 2 steps with 504 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 = -2093.2723476983 -2093.27633354187 -2093.27633786071 Force two-norm initial, final = 8.3784247 0.27826801 Force max component initial, final = 6.1528145 0.15598352 Final line search alpha, max atom move = 0.0078543705 0.0012251524 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15675 | 0.15675 | 0.15675 | 0.0 | 99.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 8.9583e-05 | 8.9583e-05 | 8.9583e-05 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003927 | | | 0.25 Nlocal: 504.000 ave 504 max 504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2332.00 ave 2332 max 2332 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: 29020.0 ave 29020 max 29020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29020 Ave neighs/atom = 57.579365 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.975 | 4.975 | 4.975 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2093.2763 0 -2093.2763 5162.3166 Loop time of 1.776e-06 on 1 procs for 0 steps with 504 atoms 168.9% 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 | | 1.776e-06 | | |100.00 Nlocal: 504.000 ave 504 max 504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2354.00 ave 2354 max 2354 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: 29020.0 ave 29020 max 29020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29020 Ave neighs/atom = 57.579365 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.975 | 4.975 | 4.975 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 -2093.2763 -2093.2763 10.815714 79.430402 7.0710179 5162.3166 5162.3166 35.414117 15410.423 41.112815 2.2721735 342.96183 Loop time of 1.42e-06 on 1 procs for 0 steps with 504 atoms 211.3% 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 | | 1.42e-06 | | |100.00 Nlocal: 504.000 ave 504 max 504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2354.00 ave 2354 max 2354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14510.0 ave 14510 max 14510 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29020.0 ave 29020 max 29020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29020 Ave neighs/atom = 57.579365 Neighbor list builds = 0 Dangerous builds = 0 504 -2093.27633786071 eV 2.27217352678143 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04