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 = 3.6580991 3.6580991 3.6580991 Created orthogonal box = (0.0000000 -43.283213 0.0000000) to (53.010893 43.283213 8.9604763) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0583878 5.5649845 5.9736509 Created 1663 atoms using lattice units in orthogonal box = (0.0000000 -43.283213 0.0000000) to (53.010893 43.283213 8.9604763) create_atoms CPU = 0.003 seconds 1663 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0583878 5.5649845 5.9736509 Created 1687 atoms using lattice units in orthogonal box = (0.0000000 -43.283213 0.0000000) to (53.010893 43.283213 8.9604763) create_atoms CPU = 0.003 seconds 1687 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 15 24 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3350 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_634187028437_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.535 | 6.535 | 6.535 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12642.567 0 -12642.567 30987.648 772 0 -13230.98 0 -13230.98 -74312.803 Loop time of 31.8977 on 1 procs for 772 steps with 3350 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 = -12642.5674548702 -13230.9692214559 -13230.9804193652 Force two-norm initial, final = 465.56324 0.33198628 Force max component initial, final = 107.17209 0.054175052 Final line search alpha, max atom move = 1.0000000 0.054175052 Iterations, force evaluations = 772 1448 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 30.86 | 30.86 | 30.86 | 0.0 | 96.75 Neigh | 0.68397 | 0.68397 | 0.68397 | 0.0 | 2.14 Comm | 0.14111 | 0.14111 | 0.14111 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2126 | | | 0.67 Nlocal: 3350.00 ave 3350 max 3350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9829.00 ave 9829 max 9829 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: 462870.0 ave 462870 max 462870 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 462870 Ave neighs/atom = 138.17015 Neighbor list builds = 22 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 772 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.535 | 6.535 | 6.535 Mbytes Step Temp E_pair E_mol TotEng Press Volume 772 0 -13230.98 0 -13230.98 -74312.803 41119.299 837 0 -13371.207 0 -13371.207 -7.1903864 39215.599 Loop time of 1.5591 on 1 procs for 65 steps with 3350 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 = -13230.9804193648 -13371.1945360901 -13371.2068777703 Force two-norm initial, final = 4076.4273 6.9706891 Force max component initial, final = 3136.7090 1.5301368 Final line search alpha, max atom move = 4.2350473e-05 6.4802018e-05 Iterations, force evaluations = 65 66 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3961 | 1.3961 | 1.3961 | 0.0 | 89.55 Neigh | 0.12027 | 0.12027 | 0.12027 | 0.0 | 7.71 Comm | 0.0061466 | 0.0061466 | 0.0061466 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03658 | | | 2.35 Nlocal: 3350.00 ave 3350 max 3350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9720.00 ave 9720 max 9720 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: 479862.0 ave 479862 max 479862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 479862 Ave neighs/atom = 143.24239 Neighbor list builds = 4 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 15 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.671 | 6.671 | 6.671 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13371.207 0 -13371.207 -7.1903864 Loop time of 2.393e-06 on 1 procs for 0 steps with 3350 atoms 167.2% 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 | | 2.393e-06 | | |100.00 Nlocal: 3350.00 ave 3350 max 3350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9611.00 ave 9611 max 9611 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: 479680.0 ave 479680 max 479680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 479680 Ave neighs/atom = 143.18806 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 15 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.671 | 6.671 | 6.671 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 -13371.207 -13371.207 51.276059 81.887286 9.3395885 -7.1903864 -7.1903864 18.330021 25.25842 -65.1596 2.3222151 4793.6015 Loop time of 2.598e-06 on 1 procs for 0 steps with 3350 atoms 230.9% 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 | | 2.598e-06 | | |100.00 Nlocal: 3350.00 ave 3350 max 3350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9611.00 ave 9611 max 9611 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 239840.0 ave 239840 max 239840 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 479680.0 ave 479680 max 479680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 479680 Ave neighs/atom = 143.18806 Neighbor list builds = 0 Dangerous builds = 0 3350 -12897.4444376609 eV 2.3222151219497 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:34