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 = 3.5200135 3.5200135 3.5200135 Created orthogonal box = (0.0000000 -52.094963 0.0000000) to (42.532485 52.094963 8.6222370) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2437310 4.9950699 5.7481580 Created 1759 atoms using lattice units in orthogonal box = (0.0000000 -52.094963 0.0000000) to (42.532485 52.094963 8.6222370) create_atoms CPU = 0.002 seconds 1759 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2437310 4.9950699 5.7481580 Created 1759 atoms using lattice units in orthogonal box = (0.0000000 -52.094963 0.0000000) to (42.532485 52.094963 8.6222370) create_atoms CPU = 0.002 seconds 1759 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 11 25 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 47 atoms, new total = 3471 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_871937946490_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 11.81 | 11.81 | 11.81 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15327.7 0 -15327.7 632.91187 51 0 -15380.83 0 -15380.83 -7039.8784 Loop time of 3.22778 on 1 procs for 51 steps with 3471 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 = -15327.6995767106 -15380.8159982996 -15380.8302920572 Force two-norm initial, final = 31.504999 0.37158352 Force max component initial, final = 3.7283136 0.083066368 Final line search alpha, max atom move = 1.0000000 0.083066368 Iterations, force evaluations = 51 96 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.162 | 3.162 | 3.162 | 0.0 | 97.96 Neigh | 0.040741 | 0.040741 | 0.040741 | 0.0 | 1.26 Comm | 0.011199 | 0.011199 | 0.011199 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01381 | | | 0.43 Nlocal: 3471.00 ave 3471 max 3471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13184.0 ave 13184 max 13184 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: 776076.0 ave 776076 max 776076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 776076 Ave neighs/atom = 223.58859 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 51 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.81 | 11.81 | 11.81 Mbytes Step Temp E_pair E_mol TotEng Press Volume 51 0 -15380.83 0 -15380.83 -7039.8784 38209.068 54 0 -15381.101 0 -15381.101 -1174.4916 38082.179 Loop time of 0.199705 on 1 procs for 3 steps with 3471 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 = -15380.8302920572 -15381.1009350419 -15381.1013514298 Force two-norm initial, final = 230.19814 0.41785722 Force max component initial, final = 164.10692 0.095398166 Final line search alpha, max atom move = 0.00022703572 2.1658791e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19597 | 0.19597 | 0.19597 | 0.0 | 98.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00058005 | 0.00058005 | 0.00058005 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003153 | | | 1.58 Nlocal: 3471.00 ave 3471 max 3471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13418.0 ave 13418 max 13418 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: 775068.0 ave 775068 max 775068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 775068 Ave neighs/atom = 223.29818 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 11.32 | 11.32 | 11.32 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15381.101 0 -15381.101 -1174.4916 Loop time of 2.024e-06 on 1 procs for 0 steps with 3471 atoms 148.2% 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 | | 2.024e-06 | | |100.00 Nlocal: 3471.00 ave 3471 max 3471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13440.0 ave 13440 max 13440 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: 775502.0 ave 775502 max 775502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 775502 Ave neighs/atom = 223.42322 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 11.32 | 11.32 | 11.32 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 -15381.101 -15381.101 42.456775 104.18993 8.6089276 -1174.4916 -1174.4916 -2.4031092 -3517.0642 -4.0073538 2.2135579 1664.9734 Loop time of 2.382e-06 on 1 procs for 0 steps with 3471 atoms 251.9% 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 | | 2.382e-06 | | |100.00 Nlocal: 3471.00 ave 3471 max 3471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13440.0 ave 13440 max 13440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 387751.0 ave 387751 max 387751 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 775502.0 ave 775502 max 775502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 775502 Ave neighs/atom = 223.42322 Neighbor list builds = 0 Dangerous builds = 0 3471 -15286.4770259487 eV 2.21355788871662 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04