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 = 2.8553246 2.8553246 2.8553246 Created orthogonal box = (0.0000000 -42.254946 0.0000000) to (34.501019 42.254946 6.9940884) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2535503 4.0518441 4.6627256 Created 876 atoms using lattice units in orthogonal box = (0.0000000 -42.254946 0.0000000) to (34.501019 42.254946 6.9940884) create_atoms CPU = 0.004 seconds 876 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2535503 4.0518441 4.6627256 Created 878 atoms using lattice units in orthogonal box = (0.0000000 -42.254946 0.0000000) to (34.501019 42.254946 6.9940884) create_atoms CPU = 0.003 seconds 878 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 24 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 1744 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_737567242631_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.560 | 5.560 | 5.560 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5337.0323 0 -5337.0323 206034.75 117 0 -7151.2325 0 -7151.2325 1487.3343 Loop time of 5.49298 on 1 procs for 117 steps with 1744 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 = -5337.03234429089 -7151.22589845493 -7151.23254863315 Force two-norm initial, final = 3362.7716 0.28410066 Force max component initial, final = 733.64857 0.043416424 Final line search alpha, max atom move = 1.0000000 0.043416424 Iterations, force evaluations = 117 210 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.3154 | 5.3154 | 5.3154 | 0.0 | 96.77 Neigh | 0.10148 | 0.10148 | 0.10148 | 0.0 | 1.85 Comm | 0.034849 | 0.034849 | 0.034849 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0412 | | | 0.75 Nlocal: 1744.00 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6959.00 ave 6959 max 6959 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: 237780.0 ave 237780 max 237780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237780 Ave neighs/atom = 136.34174 Neighbor list builds = 3 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 117 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.560 | 5.560 | 5.560 Mbytes Step Temp E_pair E_mol TotEng Press Volume 117 0 -7151.2325 0 -7151.2325 1487.3343 20392.505 121 0 -7151.4259 0 -7151.4259 -74.939107 20411.609 Loop time of 0.154745 on 1 procs for 4 steps with 1744 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 = -7151.23254863315 -7151.41875686024 -7151.42590270613 Force two-norm initial, final = 95.336468 2.7138716 Force max component initial, final = 90.378460 2.3771927 Final line search alpha, max atom move = 6.9700586e-05 0.00016569172 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15014 | 0.15014 | 0.15014 | 0.0 | 97.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00088179 | 0.00088179 | 0.00088179 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003723 | | | 2.41 Nlocal: 1744.00 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6980.00 ave 6980 max 6980 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: 237284.0 ave 237284 max 237284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237284 Ave neighs/atom = 136.05734 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.698 | 5.698 | 5.698 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7151.4259 0 -7151.4259 -74.939107 Loop time of 6.285e-06 on 1 procs for 0 steps with 1744 atoms 190.9% 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 | | 6.285e-06 | | |100.00 Nlocal: 1744.00 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6980.00 ave 6980 max 6980 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: 237128.0 ave 237128 max 237128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237128 Ave neighs/atom = 135.96789 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.698 | 5.698 | 5.698 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 -7151.4259 -7151.4259 34.463928 84.822927 6.9823114 -74.939107 -74.939107 -186.39332 -84.955867 46.531869 2.2495197 1119.2989 Loop time of 8.309e-06 on 1 procs for 0 steps with 1744 atoms 300.9% 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 | | 8.309e-06 | | |100.00 Nlocal: 1744.00 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6980.00 ave 6980 max 6980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 118564.0 ave 118564 max 118564 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 237128.0 ave 237128 max 237128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237128 Ave neighs/atom = 135.96789 Neighbor list builds = 0 Dangerous builds = 0 1744 -7151.42590270613 eV 2.24951969213222 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06