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 = 3.6063026 3.6063026 3.6063026 Created orthogonal box = (0.0000000 -42.056354 0.0000000) to (14.869166 42.056354 5.1000820) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1225980 6.1847579 5.1000820 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -42.056354 0.0000000) to (14.869166 42.056354 5.1000820) create_atoms CPU = 0.001 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1225980 6.1847579 5.1000820 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -42.056354 0.0000000) to (14.869166 42.056354 5.1000820) create_atoms CPU = 0.001 seconds 274 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 3 15 1 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 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 546 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_147603128437_004#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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 3 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 5.809 | 5.809 | 5.809 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2177.689 0 -2177.689 50481.297 89 0 -2286.0702 0 -2286.0702 10975.8 Loop time of 2.77339 on 1 procs for 89 steps with 546 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 = -2177.68902420875 -2286.06821076404 -2286.07018221506 Force two-norm initial, final = 170.78780 0.19185062 Force max component initial, final = 52.019760 0.037933146 Final line search alpha, max atom move = 0.85728355 0.032519462 Iterations, force evaluations = 89 170 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7317 | 2.7317 | 2.7317 | 0.0 | 98.50 Neigh | 0.016701 | 0.016701 | 0.016701 | 0.0 | 0.60 Comm | 0.017619 | 0.017619 | 0.017619 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007398 | | | 0.27 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9976.00 ave 9976 max 9976 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: 337464.0 ave 337464 max 337464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 337464 Ave neighs/atom = 618.06593 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 3 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 89 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.809 | 5.809 | 5.809 Mbytes Step Temp E_pair E_mol TotEng Press Volume 89 0 -2286.0702 0 -2286.0702 10975.8 6378.6005 95 0 -2286.3092 0 -2286.3092 1.3342634 6418.7652 Loop time of 0.148609 on 1 procs for 6 steps with 546 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2286.07018221507 -2286.30892266856 -2286.30916679932 Force two-norm initial, final = 90.710288 0.27455309 Force max component initial, final = 78.007811 0.044625364 Final line search alpha, max atom move = 0.00037118060 1.6564069e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14487 | 0.14487 | 0.14487 | 0.0 | 97.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00075817 | 0.00075817 | 0.00075817 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002982 | | | 2.01 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9976.00 ave 9976 max 9976 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: 337720.0 ave 337720 max 337720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 337720 Ave neighs/atom = 618.53480 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 3 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 5.946 | 5.946 | 5.946 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2286.3092 0 -2286.3092 1.3342634 Loop time of 1.842e-06 on 1 procs for 0 steps with 546 atoms 162.9% 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 | | 1.842e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9908.00 ave 9908 max 9908 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: 334152.0 ave 334152 max 334152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 334152 Ave neighs/atom = 612.00000 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 3 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 5.946 | 5.946 | 5.946 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 -2286.3092 -2286.3092 14.942434 84.037295 5.1116142 1.3342634 1.3342634 -2.1478531 3.0525211 3.0981223 2.4048432 526.04653 Loop time of 2.667e-06 on 1 procs for 0 steps with 546 atoms 225.0% 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 | | 2.667e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9908.00 ave 9908 max 9908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 167076.0 ave 167076 max 167076 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 334152.0 ave 334152 max 334152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 334152 Ave neighs/atom = 612.00000 Neighbor list builds = 0 Dangerous builds = 0 546 -2286.30916679932 eV 2.40484323178316 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03