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 = 4.0320382 4.0320382 4.0320382 Created orthogonal box = (0.0000000 -59.668717 0.0000000) to (48.719303 59.668717 9.8764362) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0064894 5.7216578 6.5842908 Created 1749 atoms using lattice units in orthogonal box = (0.0000000 -59.668717 0.0000000) to (48.719303 59.668717 9.8764362) create_atoms CPU = 0.002 seconds 1749 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0064894 5.7216578 6.5842908 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -59.668717 0.0000000) to (48.719303 59.668717 9.8764362) create_atoms CPU = 0.002 seconds 1757 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 12 28 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 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 3488 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_019873715786_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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 7.419 | 7.419 | 7.419 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11471.871 0 -11471.871 2176.3723 66 0 -11687.947 0 -11687.947 1733.9363 Loop time of 3.27545 on 1 procs for 66 steps with 3488 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11471.8707589568 -11687.9368859031 -11687.9473001418 Force two-norm initial, final = 60.170400 0.30571948 Force max component initial, final = 7.0208224 0.046814621 Final line search alpha, max atom move = 1.0000000 0.046814621 Iterations, force evaluations = 66 108 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.164 | 3.164 | 3.164 | 0.0 | 96.60 Neigh | 0.073508 | 0.073508 | 0.073508 | 0.0 | 2.24 Comm | 0.014856 | 0.014856 | 0.014856 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02306 | | | 0.70 Nlocal: 3488.00 ave 3488 max 3488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11370.0 ave 11370 max 11370 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: 603476.0 ave 603476 max 603476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 603476 Ave neighs/atom = 173.01491 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.419 | 7.419 | 7.419 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -11687.947 0 -11687.947 1733.9363 57421.962 71 0 -11688.301 0 -11688.301 -148.14734 57549.456 Loop time of 0.206732 on 1 procs for 5 steps with 3488 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 = -11687.9473001418 -11688.2906668781 -11688.3010521286 Force two-norm initial, final = 158.51801 9.3954856 Force max component initial, final = 156.88930 6.6498274 Final line search alpha, max atom move = 5.0268033e-05 0.00033427374 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20198 | 0.20198 | 0.20198 | 0.0 | 97.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0006699 | 0.0006699 | 0.0006699 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004079 | | | 1.97 Nlocal: 3488.00 ave 3488 max 3488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11379.0 ave 11379 max 11379 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: 605648.0 ave 605648 max 605648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 605648 Ave neighs/atom = 173.63761 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 12 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 7.557 | 7.557 | 7.557 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11688.301 0 -11688.301 -148.14734 Loop time of 2.501e-06 on 1 procs for 0 steps with 3488 atoms 159.9% 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 | | 2.501e-06 | | |100.00 Nlocal: 3488.00 ave 3488 max 3488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11379.0 ave 11379 max 11379 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: 605328.0 ave 605328 max 605328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 605328 Ave neighs/atom = 173.54587 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 12 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 7.557 | 7.557 | 7.557 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 -11688.301 -11688.301 48.66276 119.91512 9.8621259 -148.14734 -148.14734 -184.91629 -116.4327 -143.09302 2.5694421 2219.5284 Loop time of 2.846e-06 on 1 procs for 0 steps with 3488 atoms 316.2% 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 | | 2.846e-06 | | |100.00 Nlocal: 3488.00 ave 3488 max 3488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11379.0 ave 11379 max 11379 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 302664.0 ave 302664 max 302664 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 605328.0 ave 605328 max 605328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 605328 Ave neighs/atom = 173.54587 Neighbor list builds = 0 Dangerous builds = 0 3488 -11688.3010521286 eV 2.56944210616157 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04