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 = 3.6110509 3.6110509 3.6110509 Created orthogonal box = (0.0000000 -59.115451 0.0000000) to (41.800936 59.115451 5.1067972) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2389457 5.7350811 5.1067972 Created 1072 atoms using lattice units in orthogonal box = (0.0000000 -59.115451 0.0000000) to (41.800936 59.115451 5.1067972) create_atoms CPU = 0.003 seconds 1072 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2389457 5.7350811 5.1067972 Created 1080 atoms using lattice units in orthogonal box = (0.0000000 -59.115451 0.0000000) to (41.800936 59.115451 5.1067972) create_atoms CPU = 0.003 seconds 1080 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 9 23 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 2144 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_984358344196_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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 9 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 11.97 | 11.97 | 11.97 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8089.1817 0 -8089.1817 56116.958 80 0 -8886.8679 0 -8886.8679 3516.5692 Loop time of 5.15836 on 1 procs for 80 steps with 2144 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8089.18174822025 -8886.8604687724 -8886.86786693393 Force two-norm initial, final = 809.29193 0.36113925 Force max component initial, final = 119.32068 0.026072974 Final line search alpha, max atom move = 1.0000000 0.026072974 Iterations, force evaluations = 80 142 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.0221 | 5.0221 | 5.0221 | 0.0 | 97.36 Neigh | 0.087533 | 0.087533 | 0.087533 | 0.0 | 1.70 Comm | 0.028149 | 0.028149 | 0.028149 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02058 | | | 0.40 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16686.0 ave 16686 max 16686 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: 815280.0 ave 815280 max 815280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 815280 Ave neighs/atom = 380.26119 Neighbor list builds = 2 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 9 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.97 | 11.97 | 11.97 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -8886.8679 0 -8886.8679 3516.5692 25238.621 85 0 -8887.2258 0 -8887.2258 -16.581598 25290.13 Loop time of 0.289873 on 1 procs for 5 steps with 2144 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 = -8886.86786693395 -8887.22573024769 -8887.22575035675 Force two-norm initial, final = 194.64532 0.72786823 Force max component initial, final = 190.00548 0.47293449 Final line search alpha, max atom move = 0.00075207996 0.00035568455 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28279 | 0.28279 | 0.28279 | 0.0 | 97.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001167 | 0.001167 | 0.001167 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005915 | | | 2.04 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16706.0 ave 16706 max 16706 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: 816896.0 ave 816896 max 816896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 816896 Ave neighs/atom = 381.01493 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 9 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 11.49 | 11.49 | 11.49 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8887.2258 0 -8887.2258 -16.581598 Loop time of 2.594e-06 on 1 procs for 0 steps with 2144 atoms 154.2% 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 | | 2.594e-06 | | |100.00 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16666.0 ave 16666 max 16666 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: 816352.0 ave 816352 max 816352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 816352 Ave neighs/atom = 380.76119 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 9 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 11.49 | 11.49 | 11.49 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 -8887.2258 -8887.2258 41.947315 118.21882 5.0998837 -16.581598 -16.581598 -23.754155 3.9300752 -29.920713 2.4082907 1067.1473 Loop time of 2.999e-06 on 1 procs for 0 steps with 2144 atoms 233.4% 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 | | 2.999e-06 | | |100.00 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16666.0 ave 16666 max 16666 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 408176.0 ave 408176 max 408176 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 816352.0 ave 816352 max 816352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 816352 Ave neighs/atom = 380.76119 Neighbor list builds = 0 Dangerous builds = 0 2144 -8887.22575035675 eV 2.40829066879301 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06