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 = 4.0469996 4.0469996 4.0469996 Created orthogonal box = (0.0000000 -49.071309 0.0000000) to (40.063252 49.071309 9.9130839) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7233217 5.6744453 6.6087226 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -49.071309 0.0000000) to (40.063252 49.071309 9.9130839) create_atoms CPU = 0.002 seconds 1184 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7233217 5.6744453 6.6087226 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -49.071309 0.0000000) to (40.063252 49.071309 9.9130839) create_atoms CPU = 0.001 seconds 1184 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 12 28 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, cut 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 48 atoms, new total = 2320 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_958395190627_001#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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 5.526 | 5.526 | 5.526 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7719.0353 0 -7719.0353 1798.9295 63 0 -7768.6967 0 -7768.6967 -6215.4903 Loop time of 10.6182 on 1 procs for 63 steps with 2320 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 = -7719.03531005864 -7768.68918006013 -7768.69665757088 Force two-norm initial, final = 34.956057 0.24878317 Force max component initial, final = 4.6830850 0.032117388 Final line search alpha, max atom move = 1.0000000 0.032117388 Iterations, force evaluations = 63 120 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.601 | 10.601 | 10.601 | 0.0 | 99.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0070757 | 0.0070757 | 0.0070757 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01037 | | | 0.10 Nlocal: 2320.00 ave 2320 max 2320 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: 197424.0 ave 197424 max 197424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 197424 Ave neighs/atom = 85.096552 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.527 | 5.527 | 5.527 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -7768.6967 0 -7768.6967 -6215.4903 38977.378 68 0 -7769.1242 0 -7769.1242 -1580.2243 38742.466 Loop time of 0.618833 on 1 procs for 5 steps with 2320 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 = -7768.69665757089 -7769.1186726872 -7769.12418657958 Force two-norm initial, final = 184.59497 2.9464912 Force max component initial, final = 148.94322 2.3956711 Final line search alpha, max atom move = 9.0973159e-05 0.00021794176 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.61621 | 0.61621 | 0.61621 | 0.0 | 99.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038005 | 0.00038005 | 0.00038005 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002247 | | | 0.36 Nlocal: 2320.00 ave 2320 max 2320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6562.00 ave 6562 max 6562 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: 197952.0 ave 197952 max 197952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 197952 Ave neighs/atom = 85.324138 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 12 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 5.666 | 5.666 | 5.666 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7769.1242 0 -7769.1242 -1580.2243 Loop time of 1.989e-06 on 1 procs for 0 steps with 2320 atoms 150.8% 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 | | 1.989e-06 | | |100.00 Nlocal: 2320.00 ave 2320 max 2320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6634.00 ave 6634 max 6634 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: 198064.0 ave 198064 max 198064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 198064 Ave neighs/atom = 85.372414 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 12 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 5.666 | 5.666 | 5.666 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 -7769.1242 -7769.1242 40.001354 98.142618 9.868586 -1580.2243 -1580.2243 -69.716805 -4572.329 -98.627139 2.4129883 1711.0622 Loop time of 1.768e-06 on 1 procs for 0 steps with 2320 atoms 169.7% 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 | | 1.768e-06 | | |100.00 Nlocal: 2320.00 ave 2320 max 2320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6634.00 ave 6634 max 6634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 99032.0 ave 99032 max 99032 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 198064.0 ave 198064 max 198064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 198064 Ave neighs/atom = 85.372414 Neighbor list builds = 0 Dangerous builds = 0 2320 -7769.12418657958 eV 2.41298829769753 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11