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 = 3.6111526 3.6111526 3.6111526 Created orthogonal box = (0.0000000 -53.440179 0.0000000) to (43.633723 53.440179 8.8454813) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3795001 5.1244007 5.8969875 Created 1751 atoms using lattice units in orthogonal box = (0.0000000 -53.440179 0.0000000) to (43.633723 53.440179 8.8454813) create_atoms CPU = 0.002 seconds 1751 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3795001 5.1244007 5.8969875 Created 1759 atoms using lattice units in orthogonal box = (0.0000000 -53.440179 0.0000000) to (43.633723 53.440179 8.8454813) create_atoms CPU = 0.002 seconds 1759 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 17 40 4 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 3510 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_137964310702_004#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 17 40 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 6.744 | 6.744 | 6.744 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14478.004 0 -14478.004 30020.775 64 0 -14854.653 0 -14854.653 8634.2866 Loop time of 21.9825 on 1 procs for 64 steps with 3510 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 = -14478.0041088421 -14854.6389856943 -14854.6534849917 Force two-norm initial, final = 285.77048 0.49293428 Force max component initial, final = 40.878917 0.11709894 Final line search alpha, max atom move = 1.0000000 0.11709894 Iterations, force evaluations = 64 117 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.951 | 21.951 | 21.951 | 0.0 | 99.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.011123 | 0.011123 | 0.011123 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02086 | | | 0.09 Nlocal: 3510.00 ave 3510 max 3510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7267.00 ave 7267 max 7267 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: 189706.0 ave 189706 max 189706 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189706 Ave neighs/atom = 54.047293 Neighbor list builds = 0 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 17 40 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.744 | 6.744 | 6.744 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 -14854.653 0 -14854.653 8634.2866 41251.68 69 0 -14855.335 0 -14855.335 -46.23767 41464.365 Loop time of 1.47885 on 1 procs for 5 steps with 3510 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 = -14854.6534849917 -14855.334205372 -14855.3347787632 Force two-norm initial, final = 397.32338 2.3091521 Force max component initial, final = 298.55047 1.6066151 Final line search alpha, max atom move = 0.00020762538 0.00033357407 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4742 | 1.4742 | 1.4742 | 0.0 | 99.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049659 | 0.00049659 | 0.00049659 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004138 | | | 0.28 Nlocal: 3510.00 ave 3510 max 3510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7260.00 ave 7260 max 7260 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: 189080.0 ave 189080 max 189080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189080 Ave neighs/atom = 53.868946 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 17 41 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 6.883 | 6.883 | 6.883 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14855.335 0 -14855.335 -46.23767 Loop time of 2.183e-06 on 1 procs for 0 steps with 3510 atoms 183.2% 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 | | 2.183e-06 | | |100.00 Nlocal: 3510.00 ave 3510 max 3510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7256.00 ave 7256 max 7256 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: 188974.0 ave 188974 max 188974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188974 Ave neighs/atom = 53.838746 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 17 41 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 6.883 | 6.883 | 6.883 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 -14855.335 -14855.335 43.680338 107.26771 8.8495261 -46.23767 -46.23767 -52.275901 -62.30434 -24.13277 2.2638757 856.37614 Loop time of 2.199e-06 on 1 procs for 0 steps with 3510 atoms 227.4% 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 | | 2.199e-06 | | |100.00 Nlocal: 3510.00 ave 3510 max 3510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7256.00 ave 7256 max 7256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 94487.0 ave 94487 max 94487 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 188974.0 ave 188974 max 188974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188974 Ave neighs/atom = 53.838746 Neighbor list builds = 0 Dangerous builds = 0 3510 -14855.3347787632 eV 2.26387570008503 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:24