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 = 3.5200008 3.5200008 3.5200008 Created orthogonal box = (0.0000000 -63.363534 0.0000000) to (44.802295 63.363534 4.9780328) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0842623 5.8666679 4.9780328 Created 1298 atoms using lattice units in orthogonal box = (0.0000000 -63.363534 0.0000000) to (44.802295 63.363534 4.9780328) create_atoms CPU = 0.004 seconds 1298 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0842623 5.8666679 4.9780328 Created 1298 atoms using lattice units in orthogonal box = (0.0000000 -63.363534 0.0000000) to (44.802295 63.363534 4.9780328) create_atoms CPU = 0.004 seconds 1298 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 = 12 33 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 14 atoms, new total = 2582 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 = 12 33 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) = 6.540 | 6.540 | 6.540 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11393.091 0 -11393.091 4969.1929 55 0 -11456.607 0 -11456.607 -2569.4284 Loop time of 2.13616 on 1 procs for 55 steps with 2582 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11393.0914132391 -11456.5965807184 -11456.6067952595 Force two-norm initial, final = 49.294280 0.42943268 Force max component initial, final = 7.5962825 0.085242626 Final line search alpha, max atom move = 0.65378339 0.055730213 Iterations, force evaluations = 55 96 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.064 | 2.064 | 2.064 | 0.0 | 96.62 Neigh | 0.048704 | 0.048704 | 0.048704 | 0.0 | 2.28 Comm | 0.012494 | 0.012494 | 0.012494 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01094 | | | 0.51 Nlocal: 2582.00 ave 2582 max 2582 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13002.0 ave 13002 max 13002 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: 454792.0 ave 454792 max 454792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 454792 Ave neighs/atom = 176.13943 Neighbor list builds = 2 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 = 12 33 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 : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.541 | 6.541 | 6.541 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -11456.607 0 -11456.607 -2569.4284 28263.595 56 0 -11456.618 0 -11456.618 -1192.6983 28242.724 Loop time of 0.0660943 on 1 procs for 1 steps with 2582 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 = -11456.6067952595 -11456.6067952595 -11456.617815099 Force two-norm initial, final = 41.810059 0.80405882 Force max component initial, final = 32.699764 0.49610736 Final line search alpha, max atom move = 3.0581261e-05 1.5171588e-05 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.064703 | 0.064703 | 0.064703 | 0.0 | 97.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030216 | 0.00030216 | 0.00030216 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001089 | | | 1.65 Nlocal: 2582.00 ave 2582 max 2582 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13002.0 ave 13002 max 13002 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: 455056.0 ave 455056 max 455056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 455056 Ave neighs/atom = 176.24167 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 = 12 33 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) = 6.678 | 6.678 | 6.678 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11456.618 0 -11456.618 -1192.6983 Loop time of 1.538e-06 on 1 procs for 0 steps with 2582 atoms 195.1% 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 | | 1.538e-06 | | |100.00 Nlocal: 2582.00 ave 2582 max 2582 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13002.0 ave 13002 max 13002 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: 455096.0 ave 455096 max 455096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 455096 Ave neighs/atom = 176.25716 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 = 12 33 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) = 6.678 | 6.678 | 6.678 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 -11456.618 -11456.618 44.783878 126.72707 4.9764026 -1192.6983 -1192.6983 -28.132017 -3576.205 26.242008 2.326297 1237.7852 Loop time of 2.052e-06 on 1 procs for 0 steps with 2582 atoms 292.4% 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 | | 2.052e-06 | | |100.00 Nlocal: 2582.00 ave 2582 max 2582 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13002.0 ave 13002 max 13002 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 227548.0 ave 227548 max 227548 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 455096.0 ave 455096 max 455096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 455096 Ave neighs/atom = 176.25716 Neighbor list builds = 0 Dangerous builds = 0 2582 -11456.617815099 eV 2.32629698856507 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02