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 = 3.6473074 3.6473074 3.6473074 Created orthogonal box = (0.0000000 -44.221252 0.0000000) to (36.106501 44.221252 8.9340421) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1580716 5.1140223 5.9560280 Created 1176 atoms using lattice units in orthogonal box = (0.0000000 -44.221252 0.0000000) to (36.106501 44.221252 8.9340421) create_atoms CPU = 0.002 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1580716 5.1140223 5.9560280 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -44.221252 0.0000000) to (36.106501 44.221252 8.9340421) create_atoms CPU = 0.001 seconds 1184 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 14 34 4 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 2360 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 14 34 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.801 | 5.801 | 5.801 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9212.5818 0 -9212.5818 59222.22 77 0 -9742.0901 0 -9742.0901 12706.728 Loop time of 19.6728 on 1 procs for 77 steps with 2360 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 = -9212.5817560107 -9742.08064276457 -9742.09007979209 Force two-norm initial, final = 468.99344 0.45286367 Force max component initial, final = 67.654059 0.037261825 Final line search alpha, max atom move = 1.0000000 0.037261825 Iterations, force evaluations = 77 145 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.644 | 19.644 | 19.644 | 0.0 | 99.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010112 | 0.010112 | 0.010112 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01862 | | | 0.09 Nlocal: 2360.00 ave 2360 max 2360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5050.00 ave 5050 max 5050 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: 127504.0 ave 127504 max 127504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127504 Ave neighs/atom = 54.027119 Neighbor list builds = 0 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 14 34 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.801 | 5.801 | 5.801 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -9742.0901 0 -9742.0901 12706.728 28529.518 82 0 -9742.9854 0 -9742.9854 5.2198377 28743.133 Loop time of 1.08238 on 1 procs for 5 steps with 2360 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 = -9742.09007979208 -9742.9850152862 -9742.98540736595 Force two-norm initial, final = 396.15902 1.2468114 Force max component initial, final = 259.87708 0.69666178 Final line search alpha, max atom move = 0.00014279475 9.9479647e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.079 | 1.079 | 1.079 | 0.0 | 99.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038234 | 0.00038234 | 0.00038234 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002964 | | | 0.27 Nlocal: 2360.00 ave 2360 max 2360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5071.00 ave 5071 max 5071 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: 126736.0 ave 126736 max 126736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126736 Ave neighs/atom = 53.701695 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 14 34 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.939 | 5.939 | 5.939 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9742.9854 0 -9742.9854 5.2198377 Loop time of 2.239e-06 on 1 procs for 0 steps with 2360 atoms 178.7% 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 | | 2.239e-06 | | |100.00 Nlocal: 2360.00 ave 2360 max 2360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5044.00 ave 5044 max 5044 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: 126656.0 ave 126656 max 126656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126656 Ave neighs/atom = 53.667797 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 14 34 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.939 | 5.939 | 5.939 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 -9742.9854 -9742.9854 36.210627 88.752293 8.9437257 5.2198377 5.2198377 -38.944747 35.776829 18.827431 2.287897 866.69494 Loop time of 2.756e-06 on 1 procs for 0 steps with 2360 atoms 254.0% 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 | | 2.756e-06 | | |100.00 Nlocal: 2360.00 ave 2360 max 2360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5044.00 ave 5044 max 5044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 63328.0 ave 63328 max 63328 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 126656.0 ave 126656 max 126656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126656 Ave neighs/atom = 53.667797 Neighbor list builds = 0 Dangerous builds = 0 2360 -9742.98540736595 eV 2.28789700279613 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:21