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 = 4.0320000 4.0320000 4.0320000 Created orthogonal box = (0.0000000 -41.118493 0.0000000) to (20.559247 41.118493 4.0320000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7444415 4.7444415 4.0320000 Created 208 atoms using lattice units in orthogonal box = (0.0000000 -41.118493 0.0000000) to (20.559247 41.118493 4.0320000) create_atoms CPU = 0.001 seconds 208 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7444415 4.7444415 4.0320000 Created 210 atoms using lattice units in orthogonal box = (0.0000000 -41.118493 0.0000000) to (20.559247 41.118493 4.0320000) create_atoms CPU = 0.001 seconds 210 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 5 19 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 8.875 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 416 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_519613893196_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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 5 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 4.482 | 4.482 | 4.482 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1316.9287 0 -1316.9287 25267.557 47 0 -1392.6346 0 -1392.6346 5135.1071 Loop time of 0.854822 on 1 procs for 47 steps with 416 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1316.92874432242 -1392.63357422017 -1392.63461825875 Force two-norm initial, final = 147.22325 0.077846101 Force max component initial, final = 48.658517 0.015407995 Final line search alpha, max atom move = 1.0000000 0.015407995 Iterations, force evaluations = 47 86 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.82826 | 0.82826 | 0.82826 | 0.0 | 96.89 Neigh | 0.010528 | 0.010528 | 0.010528 | 0.0 | 1.23 Comm | 0.0091477 | 0.0091477 | 0.0091477 | 0.0 | 1.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006889 | | | 0.81 Nlocal: 416.000 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4289.00 ave 4289 max 4289 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: 73092.0 ave 73092 max 73092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73092 Ave neighs/atom = 175.70192 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 5 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.481 | 4.481 | 4.481 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -1392.6346 0 -1392.6346 5135.1071 6817.0252 52 0 -1392.7136 0 -1392.7136 -254.96388 6862.2955 Loop time of 0.0681358 on 1 procs for 5 steps with 416 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1392.63461825874 -1392.71291472629 -1392.71364325097 Force two-norm initial, final = 38.329608 2.0133901 Force max component initial, final = 26.600638 1.3820968 Final line search alpha, max atom move = 0.00052998898 0.00073249609 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.065369 | 0.065369 | 0.065369 | 0.0 | 95.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00067536 | 0.00067536 | 0.00067536 | 0.0 | 0.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002091 | | | 3.07 Nlocal: 416.000 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4274.00 ave 4274 max 4274 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: 73184.0 ave 73184 max 73184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73184 Ave neighs/atom = 175.92308 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 5 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 4.619 | 4.619 | 4.619 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1392.7136 0 -1392.7136 -254.96388 Loop time of 7.247e-06 on 1 procs for 0 steps with 416 atoms 165.6% 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 | | 7.247e-06 | | |100.00 Nlocal: 416.000 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4269.00 ave 4269 max 4269 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: 73064.0 ave 73064 max 73064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73064 Ave neighs/atom = 175.63462 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 5 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 4.619 | 4.619 | 4.619 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 -1392.7136 -1392.7136 20.567891 82.623783 4.0380769 -254.96388 -254.96388 -322.82114 -123.56141 -318.5091 2.6206543 240.71807 Loop time of 7.247e-06 on 1 procs for 0 steps with 416 atoms 248.4% 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 | | 7.247e-06 | | |100.00 Nlocal: 416.000 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4269.00 ave 4269 max 4269 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36532.0 ave 36532 max 36532 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 73064.0 ave 73064 max 73064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73064 Ave neighs/atom = 175.63462 Neighbor list builds = 0 Dangerous builds = 0 416 -1392.71364325097 eV 2.62065434465738 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01