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 = 3.4986963 3.4986963 3.4986963 Created orthogonal box = (0.0000000 -66.937501 0.0000000) to (38.644364 66.937501 6.0599198) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7016275 5.1206340 6.0599198 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -66.937501 0.0000000) to (38.644364 66.937501 6.0599198) create_atoms CPU = 0.009 seconds 1465 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7016275 5.1206340 6.0599198 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -66.937501 0.0000000) to (38.644364 66.937501 6.0599198) create_atoms CPU = 0.009 seconds 1465 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 36 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 2904 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_715003088863_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.994 | 6.994 | 6.994 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11874.361 0 -11874.361 2190.2128 55 0 -11919.738 0 -11919.738 -6827.3473 Loop time of 5.47178 on 1 procs for 55 steps with 2904 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 = -11874.3606507396 -11919.7275070928 -11919.738261486 Force two-norm initial, final = 37.125567 0.41000273 Force max component initial, final = 6.6631684 0.079096710 Final line search alpha, max atom move = 0.45658504 0.036114374 Iterations, force evaluations = 55 99 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.3493 | 5.3493 | 5.3493 | 0.0 | 97.76 Neigh | 0.06359 | 0.06359 | 0.06359 | 0.0 | 1.16 Comm | 0.029152 | 0.029152 | 0.029152 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02974 | | | 0.54 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12085.0 ave 12085 max 12085 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: 506742.0 ave 506742 max 506742 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 506742 Ave neighs/atom = 174.49793 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.994 | 6.994 | 6.994 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -11919.738 0 -11919.738 -6827.3473 31351.082 58 0 -11919.861 0 -11919.861 -3583.7132 31263.397 Loop time of 0.331057 on 1 procs for 3 steps with 2904 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 = -11919.738261486 -11919.8605349005 -11919.8614430167 Force two-norm initial, final = 113.62811 0.48031622 Force max component initial, final = 99.261509 0.077143573 Final line search alpha, max atom move = 0.00012772312 9.8530177e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32368 | 0.32368 | 0.32368 | 0.0 | 97.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015701 | 0.0015701 | 0.0015701 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005804 | | | 1.75 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12116.0 ave 12116 max 12116 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: 507648.0 ave 507648 max 507648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 507648 Ave neighs/atom = 174.80992 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.133 | 7.133 | 7.133 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11919.861 0 -11919.861 -3583.7132 Loop time of 7.657e-06 on 1 procs for 0 steps with 2904 atoms 169.8% 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 | | 7.657e-06 | | |100.00 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12140.0 ave 12140 max 12140 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: 507856.0 ave 507856 max 507856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 507856 Ave neighs/atom = 174.88154 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.133 | 7.133 | 7.133 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 -11919.861 -11919.861 38.564508 133.875 6.0554842 -3583.7132 -3583.7132 0.87658414 -10750.165 -1.8514373 2.2309978 1079.7737 Loop time of 6.876e-06 on 1 procs for 0 steps with 2904 atoms 305.4% 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 | | 6.876e-06 | | |100.00 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12140.0 ave 12140 max 12140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 253928.0 ave 253928 max 253928 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 507856.0 ave 507856 max 507856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 507856 Ave neighs/atom = 174.88154 Neighbor list builds = 0 Dangerous builds = 0 2904 -11919.8614430167 eV 2.23099778961066 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07