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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -46.785003 0.0000000) to (33.081993 46.785003 5.0449566) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1547893 5.9841282 5.0449566 Created 686 atoms using lattice units in orthogonal box = (0.0000000 -46.785003 0.0000000) to (33.081993 46.785003 5.0449566) create_atoms CPU = 0.005 seconds 686 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1547893 5.9841282 5.0449566 Created 694 atoms using lattice units in orthogonal box = (0.0000000 -46.785003 0.0000000) to (33.081993 46.785003 5.0449566) create_atoms CPU = 0.005 seconds 694 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 12 34 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1376 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_856956178669_001#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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 12 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.662 | 4.662 | 4.662 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5329.3012 0 -5329.3012 71918.46 335 0 -5809.8429 0 -5809.8429 59708.2 Loop time of 61.8223 on 1 procs for 335 steps with 1376 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5329.30120643361 -5809.83811225868 -5809.84293834114 Force two-norm initial, final = 572.09323 0.28288702 Force max component initial, final = 95.205623 0.042855900 Final line search alpha, max atom move = 1.0000000 0.042855900 Iterations, force evaluations = 335 658 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 61.592 | 61.592 | 61.592 | 0.0 | 99.63 Neigh | 0.032153 | 0.032153 | 0.032153 | 0.0 | 0.05 Comm | 0.093449 | 0.093449 | 0.093449 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1042 | | | 0.17 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5381.00 ave 5381 max 5381 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: 84096.0 ave 84096 max 84096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84096 Ave neighs/atom = 61.116279 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 12 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 335 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.662 | 4.662 | 4.662 Mbytes Step Temp E_pair E_mol TotEng Press Volume 335 0 -5809.8429 0 -5809.8429 59708.2 15616.573 352 0 -5816.4794 0 -5816.4794 624.83602 15951.967 Loop time of 1.65663 on 1 procs for 17 steps with 1376 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 = -5809.84293834114 -5816.47780348754 -5816.47940711383 Force two-norm initial, final = 1015.7938 12.011836 Force max component initial, final = 682.29312 9.0738330 Final line search alpha, max atom move = 0.00041395045 0.0037561172 Iterations, force evaluations = 17 18 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6287 | 1.6287 | 1.6287 | 0.0 | 98.31 Neigh | 0.014846 | 0.014846 | 0.014846 | 0.0 | 0.90 Comm | 0.0026293 | 0.0026293 | 0.0026293 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0105 | | | 0.63 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5229.00 ave 5229 max 5229 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: 79708.0 ave 79708 max 79708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79708 Ave neighs/atom = 57.927326 Neighbor list builds = 1 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 12 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.799 | 4.799 | 4.799 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5816.4794 0 -5816.4794 624.83602 Loop time of 6.365e-06 on 1 procs for 0 steps with 1376 atoms 188.5% 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 | | 6.365e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5235.00 ave 5235 max 5235 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: 79240.0 ave 79240 max 79240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79240 Ave neighs/atom = 57.587209 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 12 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.799 | 4.799 | 4.799 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 -5816.4794 -5816.4794 33.192148 95.079454 5.0546632 624.83602 624.83602 530.08793 431.31312 913.10701 2.4163648 2635.4647 Loop time of 7.026e-06 on 1 procs for 0 steps with 1376 atoms 298.9% 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 | | 7.026e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5235.00 ave 5235 max 5235 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39620.0 ave 39620 max 39620 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 79240.0 ave 79240 max 79240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79240 Ave neighs/atom = 57.587209 Neighbor list builds = 0 Dangerous builds = 0 1376 -5816.47940711383 eV 2.41636476095678 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:04