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 = 3.6784521 3.6784521 3.6784521 Created orthogonal box = (0.0000000 -38.583610 0.0000000) to (47.250573 38.583610 9.0103308) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0137093 5.6116264 6.0068872 Created 1325 atoms using lattice units in orthogonal box = (0.0000000 -38.583610 0.0000000) to (47.250573 38.583610 9.0103308) create_atoms CPU = 0.005 seconds 1325 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0137093 5.6116264 6.0068872 Created 1325 atoms using lattice units in orthogonal box = (0.0000000 -38.583610 0.0000000) to (47.250573 38.583610 9.0103308) create_atoms CPU = 0.005 seconds 1325 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 16 26 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 58 atoms, new total = 2592 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_024705128470_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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 16 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.549 | 5.549 | 5.549 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10803.007 0 -10803.007 1617.2914 73 0 -10902.433 0 -10902.433 -25529.635 Loop time of 1.99187 on 1 procs for 73 steps with 2592 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10803.0067540102 -10902.422249254 -10902.4326977022 Force two-norm initial, final = 47.196668 0.32451895 Force max component initial, final = 6.8778553 0.029635644 Final line search alpha, max atom move = 1.0000000 0.029635644 Iterations, force evaluations = 73 118 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8724 | 1.8724 | 1.8724 | 0.0 | 94.00 Neigh | 0.067861 | 0.067861 | 0.067861 | 0.0 | 3.41 Comm | 0.018681 | 0.018681 | 0.018681 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03288 | | | 1.65 Nlocal: 2592.00 ave 2592 max 2592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6427.00 ave 6427 max 6427 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: 199604.0 ave 199604 max 199604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199604 Ave neighs/atom = 77.007716 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 16 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 73 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.548 | 5.548 | 5.548 Mbytes Step Temp E_pair E_mol TotEng Press Volume 73 0 -10902.433 0 -10902.433 -25529.635 32853.427 92 0 -10909.591 0 -10909.591 -5124.2037 32219.038 Loop time of 0.344137 on 1 procs for 19 steps with 2592 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10902.4326977021 -10909.5908488001 -10909.5914761084 Force two-norm initial, final = 804.35095 2.1632804 Force max component initial, final = 763.78339 1.7358907 Final line search alpha, max atom move = 0.00013941432 0.00024200802 Iterations, force evaluations = 19 20 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32427 | 0.32427 | 0.32427 | 0.0 | 94.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0030473 | 0.0030473 | 0.0030473 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01682 | | | 4.89 Nlocal: 2592.00 ave 2592 max 2592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6360.00 ave 6360 max 6360 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: 199256.0 ave 199256 max 199256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199256 Ave neighs/atom = 76.873457 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 16 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.686 | 5.686 | 5.686 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10909.591 0 -10909.591 -5124.2037 Loop time of 7.217e-06 on 1 procs for 0 steps with 2592 atoms 0.0% 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 | | 7.217e-06 | | |100.00 Nlocal: 2592.00 ave 2592 max 2592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6385.00 ave 6385 max 6385 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: 200042.0 ave 200042 max 200042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200042 Ave neighs/atom = 77.176698 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 16 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.686 | 5.686 | 5.686 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 -10909.591 -10909.591 46.402127 77.16722 8.9979136 -5124.2037 -5124.2037 -84.771716 -15300.032 12.192185 2.4032685 2506.5271 Loop time of 6.926e-06 on 1 procs for 0 steps with 2592 atoms 259.9% 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 | | 6.926e-06 | | |100.00 Nlocal: 2592.00 ave 2592 max 2592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6385.00 ave 6385 max 6385 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100021.0 ave 100021 max 100021 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 200042.0 ave 200042 max 200042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200042 Ave neighs/atom = 77.176698 Neighbor list builds = 0 Dangerous builds = 0 2592 -10909.5912169084 eV 2.40326852034217 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03