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 = 3.5242205 3.5242205 3.5242205 Created orthogonal box = (0.0000000 -37.628378 0.0000000) to (21.724754 37.628378 6.1041289) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7170405 5.2811758 6.1041289 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -37.628378 0.0000000) to (21.724754 37.628378 6.1041289) create_atoms CPU = 0.003 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7170405 5.2811758 6.1041289 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -37.628378 0.0000000) to (21.724754 37.628378 6.1041289) create_atoms CPU = 0.003 seconds 458 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 = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 7 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 6.3171695 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 912 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_977363131043_005#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 = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 7 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.3171695 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) = 4.592 | 4.592 | 4.592 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3975.2845 0 -3975.2845 9495.5584 63 0 -4045.774 0 -4045.774 17967.978 Loop time of 1.05518 on 1 procs for 63 steps with 912 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 = -3975.2844976915 -4045.77092702113 -4045.77401994172 Force two-norm initial, final = 59.793924 0.16754144 Force max component initial, final = 14.914452 0.013215641 Final line search alpha, max atom move = 1.0000000 0.013215641 Iterations, force evaluations = 63 115 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0127 | 1.0127 | 1.0127 | 0.0 | 95.98 Neigh | 0.014671 | 0.014671 | 0.014671 | 0.0 | 1.39 Comm | 0.013909 | 0.013909 | 0.013909 | 0.0 | 1.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01386 | | | 1.31 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4670.00 ave 4670 max 4670 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: 78676.0 ave 78676 max 78676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78676 Ave neighs/atom = 86.267544 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 = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 7 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.3171695 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.592 | 4.592 | 4.592 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -4045.774 0 -4045.774 17967.978 9979.8509 73 0 -4046.632 0 -4046.632 -27.230473 10069.334 Loop time of 0.110013 on 1 procs for 10 steps with 912 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 = -4045.77401994174 -4046.6318899742 -4046.63196910552 Force two-norm initial, final = 221.50077 0.70310367 Force max component initial, final = 199.39479 0.36594065 Final line search alpha, max atom move = 0.00061493893 0.00022503115 Iterations, force evaluations = 10 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10352 | 0.10352 | 0.10352 | 0.0 | 94.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001308 | 0.001308 | 0.001308 | 0.0 | 1.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005181 | | | 4.71 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4696.00 ave 4696 max 4696 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: 78536.0 ave 78536 max 78536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78536 Ave neighs/atom = 86.114035 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 = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 7 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.3171695 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) = 4.730 | 4.730 | 4.730 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4046.632 0 -4046.632 -27.230473 Loop time of 6.775e-06 on 1 procs for 0 steps with 912 atoms 177.1% 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 | | 6.775e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4705.00 ave 4705 max 4705 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: 78428.0 ave 78428 max 78428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78428 Ave neighs/atom = 85.995614 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 = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 7 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.3171695 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) = 4.730 | 4.730 | 4.730 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 -4046.632 -4046.632 21.71472 75.919335 6.107931 -27.230473 -27.230473 -58.19955 -43.762653 20.270784 2.2110709 518.36662 Loop time of 7.888e-06 on 1 procs for 0 steps with 912 atoms 215.5% 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 | | 7.888e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4705.00 ave 4705 max 4705 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39214.0 ave 39214 max 39214 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 78428.0 ave 78428 max 78428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78428 Ave neighs/atom = 85.995614 Neighbor list builds = 0 Dangerous builds = 0 912 -4046.63196910551 eV 2.21107091311786 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01