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 = 4.0499992 4.0499992 4.0499992 Created orthogonal box = (0.0000000 -71.541298 0.0000000) to (41.302050 71.541298 7.0148043) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3541615 6.4200095 7.0148043 Created 1252 atoms using lattice units in orthogonal box = (0.0000000 -71.541298 0.0000000) to (41.302050 71.541298 7.0148043) create_atoms CPU = 0.007 seconds 1252 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3541615 6.4200095 7.0148043 Created 1252 atoms using lattice units in orthogonal box = (0.0000000 -71.541298 0.0000000) to (41.302050 71.541298 7.0148043) create_atoms CPU = 0.007 seconds 1252 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 ghost atom cutoff = 7 binsize = 3.5, bins = 12 41 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 2488 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_262519520678_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 12 41 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.278 | 5.278 | 5.278 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8285.2858 0 -8285.2858 3174.2228 47 0 -8320.2185 0 -8320.2185 212.15854 Loop time of 24.2792 on 1 procs for 47 steps with 2488 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 = -8285.28578048878 -8320.21130247132 -8320.21849511836 Force two-norm initial, final = 38.459737 0.24706764 Force max component initial, final = 4.7667438 0.026359754 Final line search alpha, max atom move = 1.0000000 0.026359754 Iterations, force evaluations = 47 90 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 24.242 | 24.242 | 24.242 | 0.0 | 99.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.015148 | 0.015148 | 0.015148 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02195 | | | 0.09 Nlocal: 2488.00 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7240.00 ave 7240 max 7240 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: 194176.0 ave 194176 max 194176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 194176 Ave neighs/atom = 78.045016 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 12 41 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.675 | 5.675 | 5.675 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -8320.2185 0 -8320.2185 212.15854 41454.72 48 0 -8320.2209 0 -8320.2209 566.34844 41435.72 Loop time of 0.91565 on 1 procs for 1 steps with 2488 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 = -8320.2184951183 -8320.2184951183 -8320.22086573958 Force two-norm initial, final = 14.487116 1.1585077 Force max component initial, final = 11.324970 0.86069168 Final line search alpha, max atom move = 8.8300451e-05 7.5999463e-05 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.91185 | 0.91185 | 0.91185 | 0.0 | 99.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00072259 | 0.00072259 | 0.00072259 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003076 | | | 0.34 Nlocal: 2488.00 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8371.00 ave 8371 max 8371 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: 197424.0 ave 197424 max 197424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 197424 Ave neighs/atom = 79.350482 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 ghost atom cutoff = 7 binsize = 3.5, bins = 12 41 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.813 | 5.813 | 5.813 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8320.2209 0 -8320.2209 566.34844 Loop time of 6.325e-06 on 1 procs for 0 steps with 2488 atoms 205.5% 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 | | 6.325e-06 | | |100.00 Nlocal: 2488.00 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8383.00 ave 8383 max 8383 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: 197752.0 ave 197752 max 197752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 197752 Ave neighs/atom = 79.482315 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 ghost atom cutoff = 7 binsize = 3.5, bins = 12 41 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.813 | 5.813 | 5.813 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 -8320.2209 -8320.2209 41.291517 143.0826 7.0133778 566.34844 566.34844 -28.422687 1694.1948 33.273213 2.5022359 1093.4178 Loop time of 6.836e-06 on 1 procs for 0 steps with 2488 atoms 307.2% 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 | | 6.836e-06 | | |100.00 Nlocal: 2488.00 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8383.00 ave 8383 max 8383 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 98876.0 ave 98876 max 98876 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 197752.0 ave 197752 max 197752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 197752 Ave neighs/atom = 79.482315 Neighbor list builds = 0 Dangerous builds = 0 2488 -8320.22086573958 eV 2.50223588871011 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:27