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 -44.450585 0.0000000) to (54.436121 44.450585 9.0103308) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2199020 5.4797556 6.0068872 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -44.450585 0.0000000) to (54.436121 44.450585 9.0103308) create_atoms CPU = 0.006 seconds 1756 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2199020 5.4797556 6.0068872 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -44.450585 0.0000000) to (54.436121 44.450585 9.0103308) create_atoms CPU = 0.006 seconds 1756 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 = 18 29 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 32 atoms, new total = 3480 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 = 18 29 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) = 5.693 | 5.693 | 5.693 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14506.747 0 -14506.747 9802.339 76 0 -14656.725 0 -14656.725 -9944.8864 Loop time of 2.78377 on 1 procs for 76 steps with 3480 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 = -14506.7470217628 -14656.711032911 -14656.7247412026 Force two-norm initial, final = 80.054116 0.40745181 Force max component initial, final = 8.8184963 0.068477171 Final line search alpha, max atom move = 1.0000000 0.068477171 Iterations, force evaluations = 76 133 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.628 | 2.628 | 2.628 | 0.0 | 94.41 Neigh | 0.085935 | 0.085935 | 0.085935 | 0.0 | 3.09 Comm | 0.026068 | 0.026068 | 0.026068 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04372 | | | 1.57 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8197.00 ave 8197 max 8197 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: 269796.0 ave 269796 max 269796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 269796 Ave neighs/atom = 77.527586 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 = 18 29 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 : 76 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.693 | 5.693 | 5.693 Mbytes Step Temp E_pair E_mol TotEng Press Volume 76 0 -14656.725 0 -14656.725 -9944.8864 43604.909 84 0 -14657.98 0 -14657.98 -1600.9713 43263.203 Loop time of 0.224232 on 1 procs for 8 steps with 3480 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 = -14656.7247412026 -14657.9795461503 -14657.9798984492 Force two-norm initial, final = 376.58963 0.65036186 Force max component initial, final = 340.73124 0.10382157 Final line search alpha, max atom move = 0.00015564729 1.6159547e-05 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21213 | 0.21213 | 0.21213 | 0.0 | 94.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019502 | 0.0019502 | 0.0019502 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01015 | | | 4.53 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8190.00 ave 8190 max 8190 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: 269988.0 ave 269988 max 269988 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 269988 Ave neighs/atom = 77.582759 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 = 18 29 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) = 5.831 | 5.831 | 5.831 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14657.98 0 -14657.98 -1600.9713 Loop time of 6.384e-06 on 1 procs for 0 steps with 3480 atoms 172.3% 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 | | 6.384e-06 | | |100.00 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8199.00 ave 8199 max 8199 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: 270198.0 ave 270198 max 270198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270198 Ave neighs/atom = 77.643103 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 = 18 29 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) = 5.831 | 5.831 | 5.831 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 -14657.98 -14657.98 54.061273 88.90117 9.0017082 -1600.9713 -1600.9713 -1.304505 -4799.1907 -2.4187555 2.3386462 1542.4165 Loop time of 6.746e-06 on 1 procs for 0 steps with 3480 atoms 296.5% 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 | | 6.746e-06 | | |100.00 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8199.00 ave 8199 max 8199 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 135099.0 ave 135099 max 135099 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 270198.0 ave 270198 max 270198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270198 Ave neighs/atom = 77.643103 Neighbor list builds = 0 Dangerous builds = 0 3480 -14657.9795504492 eV 2.33864617883516 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03