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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -50.582274 0.0000000) to (29.203689 50.582274 4.9600000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4928753 4.5394348 4.9600000 Created 622 atoms using lattice units in orthogonal box = (0.0000000 -50.582274 0.0000000) to (29.203689 50.582274 4.9600000) create_atoms CPU = 0.002 seconds 622 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4928753 4.5394348 4.9600000 Created 627 atoms using lattice units in orthogonal box = (0.0000000 -50.582274 0.0000000) to (29.203689 50.582274 4.9600000) create_atoms CPU = 0.001 seconds 627 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 = 11 37 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 1 atoms, new total = 1248 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_058735400462_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 = 11 37 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) = 4.639 | 4.639 | 4.639 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4804.0263 0 -4804.0263 73794.673 102 0 -5333.1633 0 -5333.1633 5229.0941 Loop time of 5.46786 on 1 procs for 102 steps with 1248 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4804.02629743191 -5333.16038297688 -5333.16329209688 Force two-norm initial, final = 845.79811 0.32817974 Force max component initial, final = 227.22915 0.098945362 Final line search alpha, max atom move = 1.0000000 0.098945362 Iterations, force evaluations = 102 185 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.4314 | 5.4314 | 5.4314 | 0.0 | 99.33 Neigh | 0.010974 | 0.010974 | 0.010974 | 0.0 | 0.20 Comm | 0.01258 | 0.01258 | 0.01258 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01292 | | | 0.24 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5155.00 ave 5155 max 5155 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: 72736.0 ave 72736 max 72736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72736 Ave neighs/atom = 58.282051 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 = 11 37 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 : 102 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.639 | 4.639 | 4.639 Mbytes Step Temp E_pair E_mol TotEng Press Volume 102 0 -5333.1633 0 -5333.1633 5229.0941 14653.715 105 0 -5333.2553 0 -5333.2553 -1.2370613 14697.327 Loop time of 0.192612 on 1 procs for 3 steps with 1248 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 = -5333.16329209688 -5333.25179793336 -5333.25532669893 Force two-norm initial, final = 87.264702 0.42108534 Force max component initial, final = 66.813497 0.13208787 Final line search alpha, max atom move = 8.1188449e-05 1.0724009e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19074 | 0.19074 | 0.19074 | 0.0 | 99.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028936 | 0.00028936 | 0.00028936 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001583 | | | 0.82 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5150.00 ave 5150 max 5150 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: 72692.0 ave 72692 max 72692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72692 Ave neighs/atom = 58.246795 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 = 11 37 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) = 4.777 | 4.777 | 4.777 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5333.2553 0 -5333.2553 -1.2370613 Loop time of 1.915e-06 on 1 procs for 0 steps with 1248 atoms 156.7% 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 | | 1.915e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5150.00 ave 5150 max 5150 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: 72672.0 ave 72672 max 72672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72672 Ave neighs/atom = 58.230769 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 = 11 37 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) = 4.777 | 4.777 | 4.777 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 -5333.2553 -5333.2553 29.200095 101.37237 4.9651743 -1.2370613 -1.2370613 5.0411371 5.6617863 -14.414107 2.3255443 714.20647 Loop time of 2.262e-06 on 1 procs for 0 steps with 1248 atoms 221.0% 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 | | 2.262e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5150.00 ave 5150 max 5150 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36336.0 ave 36336 max 36336 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 72672.0 ave 72672 max 72672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72672 Ave neighs/atom = 58.230769 Neighbor list builds = 0 Dangerous builds = 0 1248 -5333.25532669893 eV 2.32554432195756 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06