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 = 3.6150002 3.6150002 3.6150002 Created orthogonal box = (0.0000000 -58.736800 0.0000000) to (11.989599 58.736800 8.8549058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4498178 5.3397091 5.9032705 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -58.736800 0.0000000) to (11.989599 58.736800 8.8549058) create_atoms CPU = 0.004 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4498178 5.3397091 5.9032705 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -58.736800 0.0000000) to (11.989599 58.736800 8.8549058) create_atoms CPU = 0.003 seconds 530 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 4 31 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1056 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_020851069572_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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 4 31 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.094 | 5.094 | 5.094 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3629.7865 0 -3629.7865 11285.613 79 0 -3727.079 0 -3727.079 4770.4928 Loop time of 2.75992 on 1 procs for 79 steps with 1056 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 = -3629.78647378499 -3727.07577464593 -3727.07897337399 Force two-norm initial, final = 56.756559 0.19767308 Force max component initial, final = 8.5934384 0.055842980 Final line search alpha, max atom move = 1.0000000 0.055842980 Iterations, force evaluations = 79 146 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6908 | 2.6908 | 2.6908 | 0.0 | 97.50 Neigh | 0.024624 | 0.024624 | 0.024624 | 0.0 | 0.89 Comm | 0.023499 | 0.023499 | 0.023499 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.021 | | | 0.76 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6410.00 ave 6410 max 6410 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: 178984.0 ave 178984 max 178984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 178984 Ave neighs/atom = 169.49242 Neighbor list builds = 1 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 4 31 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.100 | 5.100 | 5.100 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -3727.079 0 -3727.079 4770.4928 12471.793 84 0 -3727.2204 0 -3727.2204 -395.1081 12518.425 Loop time of 0.120166 on 1 procs for 5 steps with 1056 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 = -3727.07897337401 -3727.21807857496 -3727.22035905902 Force two-norm initial, final = 73.984988 5.9746127 Force max component initial, final = 66.912275 4.9818786 Final line search alpha, max atom move = 0.00014274118 0.00071111922 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11569 | 0.11569 | 0.11569 | 0.0 | 96.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00108 | 0.00108 | 0.00108 | 0.0 | 0.90 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003395 | | | 2.83 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6648.00 ave 6648 max 6648 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: 180884.0 ave 180884 max 180884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180884 Ave neighs/atom = 171.29167 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 4 31 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.238 | 5.238 | 5.238 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3727.2204 0 -3727.2204 -395.1081 Loop time of 6.646e-06 on 1 procs for 0 steps with 1056 atoms 180.6% 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 | | 6.646e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6651.00 ave 6651 max 6651 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: 179776.0 ave 179776 max 179776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179776 Ave neighs/atom = 170.24242 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 4 31 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.238 | 5.238 | 5.238 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 -3727.2204 -3727.2204 11.982921 118.01187 8.8524057 -395.1081 -395.1081 -637.25292 -157.62789 -390.44349 2.2700253 429.65818 Loop time of 7.166e-06 on 1 procs for 0 steps with 1056 atoms 265.1% 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 | | 7.166e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6651.00 ave 6651 max 6651 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 89888.0 ave 89888 max 89888 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 179776.0 ave 179776 max 179776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179776 Ave neighs/atom = 170.24242 Neighbor list builds = 0 Dangerous builds = 0 1056 -3727.22035905902 eV 2.27002530936756 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03